Question : Javascript library

Has there been any work towards converting the code from processing to javascript.

Nope.

Cool. thanks for the info!. I did start porting to JS and ran into some snags so i thought id ask before i went any further. not for the faint of heart.

Yeah - it's not as bad as most CFD codes, but it's not a walk-in-the-park
either. I have put a few fluids things in JS.
https://weymouth.github.io/fluid-dynamics/
Gabriel D Weymouth

"Computers are useless. They can only give you answers." Pablo Picasso
On Tue, Oct 5, 2021 at 8:05 AM ThreePointSquare @.***>
wrote:

Cool. thanks for the info!. I did start porting to JS and ran into some
snags so i thought id ask before i went any further. not for the faint of
heart.
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[LiveComponent] set LiveArg value to null if empty string

Checks the type to see if the argument is nullable and is not a string, if so, and an empty string is provided, the value will be overwritten to null. This should be backwards compatible since before users were manually casting to string "null" in this case.

Q
A

Bug fix?
kinda?

New feature?
kinda?

Issues
Fix #1691

License
MIT

Includes type information in the LiveArg attribute, this type information is then used in the controller subscriber of LiveAction to convert empty strings ("") to null, only when null is accepted and the types does not allow string.

I'll fix code style if given green light by maintainers.

I need to look in depth but this implementation seems  at first a bit overkill to me...  and it changes information in the request (not sure if we want that).
I'll be back to you in a day or two :)

I need to look in depth but this implementation seems at first a bit overkill to me...

Absolutely 100% agree, like I also said on the issue:

Imho it's a bit convoluted since we need to keep actual empty strings into account and can't just blindly convert.

it changes information in the request

yeah I looked at a couple of options but if we want to stay within LiveComponent and not modify Symfony’s parameter converter or the way twig inserts null into the dom this was the only way afaik :/ if you know any other places we could hook into to change the values that’d be great.
Thanks for looking into it and lmk if you got any suggestions

Pure curiosity, in your original case, how does it behave in the following cases:

you explicitely set null as default value

    #[LiveAction]
    public function action(#[LiveArg] ?int $id = null): void

You dont send the argument

    {% if parentId %}
    data-live-parent-id-param="{{ parentId }}"
    {% endif %}

This works, even without setting a default argument I think? Although it doesn’t look very elegant :/

Bonus (even if i'm 99% sure this wont change a thing) - You echo nothing when parentId is null

    data-live-parent-id-param="{{ parentId ? parentId }}"

I have no hope it changes radically things, but some may be leads to temporary solutions :)

I’m not sure this is valid twig syntax? 😅

(parenthesis: you can write {{ parentId ?? 'null' }} instead of your ternary expression)

this is actually what I’ve settled at for now.
I suppose the larger issue at hand is the fact that we lose all type information due to the way parameters are done now using data attributes. We have no way of figuring out what went into the param and thus need complex logic to “guess” 1. what the original type was and 2. what the LiveAction expects it to be.
Symfony’s controller arguments don’t have that issue because the way routing works, you can’t really have a url param with empty string, that’s the same as leaving it out altogether. In which case the router won’t match unless a default value is provided (either route default or PHP default). But here in LiveComponent it is possible to have an empty string as a value to a parameter that may not expect strings.
We also need to keep in mind that Twig may not be the only source for LiveComponent, they can also be created from JS or just plain html.
Side question; how did the old LiveArgs handle this? I can’t remember it being an issue in the pre-stable “parsed” solution..
So to tl;dr, controller arguments takes care of most type coercions, except for empty string when string is not in the type, because this is a case they don’t need to deal with in routing.
I suppose the question Is if this is something we want to tackle here?

I’m not sure this is valid twig syntax? 😅

I'm pretty sure it is ;)

you can’t really have a url param with empty string, that’s the same as leaving it out altogether.

That is an interesting point. So (imagine no BC here for simplicity) what you say is: we could purely filter arguments for empty values (null / empty string) ?

you can’t really have a url param with empty string

No, but the same problem applies to query string parameters in controller (that is pretty much the same thing here, as there is no path parameters in LiveActions

you can’t really have a url param with empty string, that’s the same as leaving it out altogether.

That is an interesting point. So (imagine no BC here for simplicity) what you say is: we could purely filter arguments for empty values (null / empty string) ?

Yes, then if the LiveArg expects a string, the LiveArg can have a default empty string value (string $val = “”), if it’s nullable, regardless of the type, it can have a default null. That could work.

No, but the same problem applies to query string parameters in controller

That is correct, but query parameters are accessed through the request object, with a second param to set a default value. And I think their value is always string unless a different default value is given or they’re modified by an event subscriber along the way (like in this PR). So it’s always up to the user to cast/parse/… it into the type they need and do error handling accordingly.

Yes, then if the LiveArg expects a string, the LiveArg can have a default empty string value (string $val = “”), if it’s nullable, regardless of the type, it can have a default null. That could work.

So (always in this "if" scenario) the only difficulty would be to handle BC with empty strings for arguments with no default values, right ?
#[LiveAction]
public function foo(#[LiveArg] string $bar)

Let's sleep on it (at least, i'm going to 😅 ) and see tomorrow how this can be done :)

That is correct [...]

Yep, you're right !

Let's sleep on it

yep same 😅. I got some ideas I’ll try out tomorrow to simplify the implementation. I really like the result that this PR brings, but I’m quite unhappy with the implementation itself. As you stated, it’s overkill and perhaps just be simplifying everything we can find something that works without a BC break.

Alright, was able to simplify a few things, and I don't think I dislike it as much anymore.
I've cleaned up the loop in the subscriber, and now LiveArg actually does what it advertises it does, gathering the live arguments. instead of only returning the argument names.
Lmk what you think.

I'll look tomorrow (too many things right now) but this seems really clean!

Just realizing...  there may be a simpler solution.
As LiveActions are controller methods, would an ArgumentResolver/ValueResolver be a better place to handle this conversion ?
Type would be available in metadata, avoiding the reflection things in LiveArg class...
We would just have to check the nullable from LiveAction arguments (without even looking at LiveArgs)..
WDYT ?
I can look this week-end if you have no time until then (or are fed up with this PR haha)

@smnandre

As LiveActions are controller methods, would an ArgumentResolver/ValueResolver be a better place to handle this conversion ?

@WebMamba

LiveComponent are Symfony controller, so you should easily get the value and the type of your argument. Then if you don't have a value and the type is nullable you set it to null. Tell me if that helps.

Yeah this is actually what I thought LiveArgs was already using under the hood for the custom name conversion before I started investigating this issue. But since the liveArgs function on LiveArg already existed, and it already used Reflection and loops over all arguments, there'd be little overhead to add this typecheck.
I'd have to play around a bit with the value/argument resolvers on scalar types, and what metadata is provided to see if this could help us in this case, and make sure they're only active on live actions, and not globally (it could interfere with userland controllers too?)

I can look this week-end if you have no time until then (or are fed up with this PR haha)

I'd love to continue working on it, but if you beat me to it then it's fair game 😄

I'd love to continue working on it

So keep working on it, there is no hurry. This is good to meet new people bringing new ideas 😁

Why not take inspiration from MapEntity, and make LiveArg extends ValueResolver ?

@smnandre Updated but it's not immediately obvious to me what the added benefit is except for the disabled option and it's still got the issue with different Symfony versions.

and it's still got the issue with different Symfony versions.

Here's an option to support all versions of Symfony:

https://github.com/zenstruck/filesystem/blob/b344aa80c4af020aa3901edb49a40ebb64f348a8/src/Filesystem/Symfony/HttpKernel/PendingFileValueResolver.php
https://github.com/zenstruck/filesystem/blob/b344aa80c4af020aa3901edb49a40ebb64f348a8/src/Filesystem/Symfony/HttpKernel/PendingFileValueResolverTrait.php

@smnandre , @WebMamba ,
Alright, added the ValueResolver like in MapEntity and added BC for Symfony < 6.2. CS passes and all tests pass. Since this resolver is used in like 90% of tests I didn't write an explicit test for it, but I did add the "empty string passed to nullable non string" case to existing tests.
It's been a pleasure and I learnt some new things, if there's some minor changes you guys want let me know, but I'm not going to keep on re-implementing the same fix in different ways, I suggest we go with this and do a refactor/improvements later down the line when Symfony 6.2 isn't supported anymore and we can get rid of the <class/property/interface>_exists checks.

Thank you @jannes-io.

Awesome. Thanks to all for the pointers and review.

Thank you for this great PR !

Hi @kbond , whoops, I didn't know that you could use non-scalar values for LiveArgs.
So I suppose the _component_action_args attributes are not being set as global request attributes anymore, so even disabling the LiveArgValueResolver will not return the old behavior.
A possible/controversial solution?
Perhaps in the supports method of LiveArgValueResolverTrait we could, after confirming that it's a LiveArg, move the value from _component_action_args to just the attributes but not return any values. Then the doctrine MapEntity will run, and the value will be where MapEntity expects it to be, and returns the value.
Although I'm not a fan of mutating the request like that, I think it should work theoretically... Let me know if you want me to try and conjure up a test/fix that would do this.
Spent some time looking at ArgumentResolver and HttpKernel and it seems like in ArgumentResolver it's possible that multiple values are returned for 1 argument. And a little later all arguments are passed as args to the controller. What happens in this case? Where do the values go?

I really think we have here a specific edge case with batch and subrequests.


Solution: "status": "Failed",  "code": "VaultNameNotValid",

Hi Everyone.
I found this error. The rason for this error you can found in this link: https://go.microsoft.com/fwlink/?linkid=2147742. in short, it is required to add a number to the end of the automation variable.
You can make this:

In Base Resource Name => ABCD-AB
in var: -vault2023
The name completed for this deploy: ABCD-AB-Communicator23

You can see the var to modify in: Edit template=>Vars=>keyvaultName

Add charter to first and a number to end of var vault.
for example: -vault2023

and Save
I'm very new in git so i put this useful information in this section.
Thanks you.

Thanks you.


Clean up unary option declaration

There shouldn't be two different syntaxes when declaring them.
The for keyword should be removed.
From there

Yet to be released

@MathieuAA when is it supposed to release this change? We could also make the "for" keyword optional as this is a breaking change for existing projects.

@colameo Hi, yeah I know and sorry about that. It was already released (v1.4.0)


try reducing assumptions for closing game; minimise cases in solver

I tried removing some assumptions in a random fashion from the closing game input. It turns out that the infinitesimal constraints are all necessary, but that some of the others are not. However, removing these constraints significantly increases the number of case splits required - when I reached 525 (!) I stopped, but I could imagine that more could be removed in exchange for even more case splits.
I wondered if the number of splits could be reduced by weakening the assumptions of the current case split and seeing if there was still a solution. It can (525 -> 52), but it's quite expensive.
I'm don't think either of these changes want to be in the mainline, but you may find them interesting.

This got subsumed by other development. No bad thing!


SDCard - HAL_SD_ERROR_RX_OVERRUN with .bss in DTCMRAM

It has taken me a while to track this one down!
Trying to read from the SDCard when .bss is in DTCMRAM causes a HAL_SD_ERROR_RX_OVERRUN, this is set in the interrupt handler HAL_SD_IRQHandler() and caused by a SDMMC_IT_RXOVERR.
The sram linker script is putting .bss in DTCMRAM, I guess there must be some static vars that do not like being in here effecting it.
Change this to SRAM and everything works fine.

Thanks for bringing this up. The SDMMC is unique in that it has limited access to on-board memories:

So you can use the SRAM, or the external SDRAM for FIL objects, etc. that directly interact with the SDMMC1 data registers.
It might be worth separating off a small chunk of space within the SRAM-execution linker that can still be used for SDMMC accesses. However, the user would still have to know to place them there.

Hi Stephan,
I am also having problems unrelated to this with SDCard access.
Just using the normal flash linker script I am getting the same SDMMC_IT_RXOVERR when calling f_read(), also f_write() is failing silently.
The reads from the f_mount previously work fine, as do f_open() and f_close()
Very strange, I will knock up a basic test case tomorrow that maybe someone else could test, maybe there is an issue with my field.
I have tried changing to Speed::Slow to see if that helps but it didn't.

@AndrewCapon hmm, that sounds like what may happen if you're allocating any of the FIL, DIR, or FATFS objects on the stack or heap (which is in DTCMRAM by default).
The new FatFSInterface object has a global FATFS instance available for each possilbe media (SDMMC / USB) that have their own getters.
For FIL and DIR objects that will directly touch the SDMMC, I usually declare them all somewhere globally so that they end up in the AXI SRAM region.
If you are getting the error and have verified that any such objects are located in AXI SRAM then there may be another issue, and our team can certainly look into it further.

Hi @stephenhensley
You are spot on, all working now. Thanks very much for the info.
Andy


[UI] - Namespaces' names no longer displayed

Is there an existing issue for this?

[X] I have searched the existing issues

Current Behavior
Cypress expects to see all namespaces' names and since last night, the names are not displayed anymore.

We think the UI should be adapted to match the changes in https://github.com/epinio/epinio/pull/1462 (new meta field?)
Expected Behavior
We should see all namespaces' names.
Steps To Reproduce
No response
Environment
- OS: Linux
- Architecture: x86_64
- Epinio Version: main
- Epinio UI Version: latest release

Logs
No error/warning message spotted.

Anything else?
No response

As per slack conversation this is the result of the API rework. There's some of this still to come (https://github.com/epinio/epinio/issues?q=is%3Aissue+is%3Aopen+label%3Aapi).
I'd like to wait until all the breaking changes are in before addressing these. I'd also need to get the unreleased code running (or there's a release and the UI is temporarily broken)

It's fixed in the latest epinio-dev branch.


gptscript: 0.1.1 -> 0.5.0

Description of changes

Bump from 0.1.1 to 0.5.0
Fix version flag
Format with nixfmt-rfc-style

Things done

Built on platform(s)

[ ] x86_64-linux
[ ] aarch64-linux
[ ] x86_64-darwin
[ ] aarch64-darwin

For non-Linux: Is sandboxing enabled in nix.conf? (See Nix manual)

[ ] sandbox = relaxed
[ ] sandbox = true

[ ] Tested, as applicable:

NixOS test(s) (look inside nixos/tests)
and/or package tests
or, for functions and "core" functionality, tests in lib/tests or pkgs/test
made sure NixOS tests are linked to the relevant packages

[ ] Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
[ ] Tested basic functionality of all binary files (usually in ./result/bin/)
24.05 Release Notes (or backporting 23.05 and 23.11 Release notes)

[ ] (Package updates) Added a release notes entry if the change is major or breaking
[ ] (Module updates) Added a release notes entry if the change is significant
[ ] (Module addition) Added a release notes entry if adding a new NixOS module

[ ] Fits CONTRIBUTING.md.

Add a :+1: reaction to pull requests you find important.

Result of nixpkgs-review pr 305899 run on x86_64-linux 1

1 package built:

gptscript


feat: Add strapp.click.sentry.capture_usage_errors

Pull Request Test Coverage Report for Build<PHONE_NUMBER>

27 of 29 (93.1%)  changed or added relevant lines in 1 file are covered.
No unchanged relevant lines lost coverage.
Overall coverage decreased (-0.1%) to 90.122%

Changes Missing Coverage
Covered Lines
Changed/Added Lines
%

src/strapp/click/sentry.py
27
29
93.1%

Totals

Change from base Build<PHONE_NUMBER>:
-0.1%

Covered Lines:
833

Relevant Lines:
912

💛  - Coveralls


Throw exception on undefined config value

Lots of places in the code use CTX('config')->get(...) (OpenXPKI::Config) which just returns undef if the specified key does not exist. Some code checks the return value, some doesn't. This can lead to errors very hard to track.
get() should throw an exception if the key is unknown and we could introduce a two parameter version where a default value can be supplied:
CTX('config')->get('non.existing')    # throws exception
CTX('config')->get('non.existing', 5) # returns 5

Dont do this! If it matters, check the return value!
CTX('config') is a reference to a "Connector" (or to be more precise to a set of nested connectors).
The connector base class offers the boolean option "die on undef" and it is used in many places that return values can just be undef/empty. Most connectors also offer the "exist" method call to check for the existence of a parameter without getting its value.
See https://github.com/mrscotty/connector/blob/master/lib/Connector.pm to get enlightened on the power of connectors :)


REFACTOR(runtime): use RecordBatch to represent query results

Current runtime code uses BaseDataBlock to represent query results, which is a simple wrapper around the Vec<u8> buffer. This straightforward representation does not enable easy element-wise data indexing, which is required for performing type conversion for the MySQL server.
This commit instead uses Arrow::RecordBatch to store query results, which provides good element-wise access API on top of the Arrow data format used by TB.
Note that our original BaseDataBlock is still useful as a "fast path". Where we do not need element-wise data access (e.g., INSERT queries), we can still use BaseDataBlock to directly store the data buffer.

This straightforward representation does not enable easy element-wise data indexing, which is required for performing type conversion for the MySQL server.

let's a quick discuss: can you show the idea or the codes why element-wise data indexing is required for type conversion for the MySQL server?

@jinmingjian Thanks for your comments! Here are the reasons why I think element-wise access is necessary.

MySQL's client-server uses a row-based data format [1, 2] (ResultSet Rows), whereas TB internally uses columnar storage. We need element-wise indexing to derive the ith row out of given columns.
The msql-srv crate that we use only provide APIs to write a single result element or entire row. We need to get the value of each result element in order to write the result set.

[1] https://dev.mysql.com/doc/internals/en/binary-protocol-resultset-row.html
[2] https://mariadb.com/kb/en/result-set-packets/

@fandahao17 thanks for sharing. In fact, we only need element-wise indexing in returning the results to the MySQL client. Right?

Currently yes. But I guess it will also be required if we want to support other protocols. Converting MySQL response back to TB's Block also seems painful (engine/mysql.rs).
I'm curious why we didn't use Arrow's RecordBatch and Array at the beginning, because they seem to be a more feature-rich version of TB's Block and Column. In fact we do use RecordBatch and Array to do queries in DataFusion, but we convert them into Block after we get the query result.
If we have clear reasons to stick to Block and Column, I can keep the usage of RecordBatch to a minimum and only convert Block to RecordBatch in the MySQL module.

@fandahao17 "Not reason to use" is the reason "not to use" :smile: 99% abstractions can not been done with zero overhead. RecordBatch is just one of them(especially in element-wise indexing). Feature-rich has its price. But considered you are not using this everywhere, I will let your PR go to make the further changes.

Thanks. I will follow on the performance implications of this change.
发自我的iPhone

在 2021年9月6日，下午5:03，Jin Mingjian @.***> 写道：

@fandahao17 "Not reason to use" is the reason "not to use" 😄 99% abstractions can not been done with zero overhead. RecordBatch is just one of them(especially in element-wise indexing). Feature-rich has its price. But considered you are not using this everywhere, I will let your PR go to make the further changes.
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sub entites are not in right structure

I'm using version 2.6.3 and I have this transaction
`            using (var transaction = DbContext.Database.BeginTransaction())
{
DbContext.BulkInsert(availables, bulkConfig);
foreach (var available in availables)
{
foreach (var hotel in available.Hotels)
{
hotel.AvailableId = available.Id;
}
hotels.AddRange(available.Hotels);
}
DbContext.BulkInsert(hotels, bulkConfig);
            foreach (var hotel in hotels)
            {
                foreach (var room in hotel.Rooms)
                {
                    room.HotelId = hotel.Id;
                }
                foreach (var suggest in hotel.SuggestedRooms)
                {
                    suggest.HotelId = hotel.Id;
                }
                rooms.AddRange(hotel.Rooms);
                suggests.AddRange(hotel.SuggestedRooms);
            }
            DbContext.BulkInsert(rooms);
            DbContext.BulkInsert(suggests);

            transaction.Commit();
        }`

but hotels available id change to another available in DB.
I have to say hotels in Available objects are ICollection.

I changed
        private static Expression<Func<DbContext, IQueryable<T>>> OrderBy<T>(Expression<Func<DbContext, IQueryable<T>>> source, string ordering)         {             Type entityType = typeof(T);             PropertyInfo property = entityType.GetProperty(ordering);             ParameterExpression parameter = Expression.Parameter(entityType);             MemberExpression propertyAccess = Expression.MakeMemberAccess(parameter, property);             LambdaExpression orderByExp = Expression.Lambda(propertyAccess, parameter);             MethodCallExpression resultExp = Expression.Call(typeof(Queryable), "OrderBy", new Type[] { entityType, property.PropertyType }, source.Body, Expression.Quote(orderByExp));             return Expression.Lambda<Func<DbContext, IQueryable<T>>>(resultExp, source.Parameters);         }
to =>
        private static Expression<Func<DbContext, IQueryable<T>>> OrderBy<T>(Expression<Func<DbContext, IQueryable<T>>> source, string ordering)         {             Type entityType = typeof(T);             PropertyInfo property = entityType.GetProperty(ordering);             ParameterExpression parameter = Expression.Parameter(entityType);             MemberExpression propertyAccess = Expression.MakeMemberAccess(parameter, property);             LambdaExpression orderByExp = Expression.Lambda(propertyAccess, parameter);             MethodCallExpression resultExp = Expression.Call(typeof(Queryable), "OrderByDescending", new Type[] { entityType, property.PropertyType }, source.Body, Expression.Quote(orderByExp));             return Expression.Lambda<Func<DbContext, IQueryable<T>>>(resultExp, source.Parameters);         }
And it's work fine.
any Comment?

Hello,
I am having the same issue. Could you please write where had you changed the code? And maybe why changing orderBy into OrderByDescending is fixing this?
thanks

I've just raised a new issue https://github.com/borisdj/EFCore.BulkExtensions/issues/264 but it might be the same problem you are experiencing.

Hello,
I am having the same issue. Could you please write where had you changed the code? And maybe why changing orderBy into OrderByDescending is fixing this?
thanks

In the file tableinfo.cs, towards the end in the method called OrderBy

I have added comment to issue 264.
Check if that solves this issue as well.


Cannot change column type in project table view

What happened?
I can't change the column type in the project column view.  This requires me to create a db folder view to make these edits.  I'm unsure if this is by design or a bug?
What did you expect to happen?
I expected that when selecting the type under configure field that the drop down would allow me to change to a select or other property. I attempted to add some default values to see if that would trigger the drop down, and it had no effect.
How can we reproduce it (as minimally and precisely as possible)?
Load a project, I am using the same sample budget project created for other issue(s).  Select the three dots and then configure field.  nothing happens when clicking the text drop down.

Anything else we need to know?
No response
Plugin version
1.11.5
Obsidian version
1.1.9
OS
Windows

Changing column type isn't supported yet. Sounds like a duplicate of #320?

Thanks.  I'll get better at search keywords before posting. :)

No worries. I'd prefer to err on the side of duplicates rather than losing out on a bug report 😄


Game crashed when I used the Oath of Altruism paladin subclass reaction to take ally's damage for the first time

Game crashed when I used the Oath of Altruism paladin subclass reaction to take ally's damage for the first time.
It crashed the game and when I reloaded the last save, it crashed again with an error message stating my save data has been corrupted. Then I looked at the file and saw this crash report:
Uploading Crash Report
ArgumentNullException: Value cannot be null.
Parameter name: key
at System.Collections.Generic.Dictionary2[TKey,TValue].TryInsert (TKey key, TValue value, System.Collections.Generic.InsertionBehavior behavior) [0x00008] in <eae584ce26bc40229c1b1aa476bfa589>:0    at System.Collections.Generic.Dictionary2[TKey,TValue].Add (TKey key, TValue value) [0x00000] in :0
at GameLocationCharacter.SerializeReferenceDictionary[T] (IElementsSerializer serializer, IVersionProvider versionProvider, System.Collections.Generic.Dictionary2[TKey,TValue] dict, System.String dictName) [0x000d6] in <10624896cb4e451583b5b6d9ca571f3a>:0    at GameLocationCharacter.SerializeElements (IElementsSerializer serializer, IVersionProvider versionProvider) [0x00131] in <10624896cb4e451583b5b6d9ca571f3a>:0    at BinarySerializer.SerializeElement[T] (System.String elementName, T value, Serializer+SerializationOption serializationOptions) [0x00217] in <10624896cb4e451583b5b6d9ca571f3a>:0  Rethrow as Exception: An exception has been thrown during the deserialization of an element of type GameLocationCharacter (serialization type: GameLocationCharacter)   at BinarySerializer.SerializeElement[T] (System.String elementName, T value, Serializer+SerializationOption serializationOptions) [0x0045e] in <10624896cb4e451583b5b6d9ca571f3a>:0    at Serializer.SerializeSubElement[T] (System.String elementName, T value, Serializer+SerializationOption serializationOptions) [0x00111] in <10624896cb4e451583b5b6d9ca571f3a>:0    at BinarySerializer.SerializeElement[T] (System.String elementName, System.Collections.Generic.List1[T] list, System.String subElementName, Serializer+SerializationOption serializationOptions) [0x001ee] in <10624896cb4e451583b5b6d9ca571f3a>:0
at Serializer.SerializeElement[T] (System.String elementName, System.Collections.Generic.List1[T] list) [0x00000] in <10624896cb4e451583b5b6d9ca571f3a>:0    at GameLocationCharacterManager.SerializeElements (IElementsSerializer serializer, IVersionProvider versionProvider) [0x00000] in <10624896cb4e451583b5b6d9ca571f3a>:0    at BinarySerializer.SerializeElement[T] (System.String elementName, T value, Serializer+SerializationOption serializationOptions) [0x00217] in <10624896cb4e451583b5b6d9ca571f3a>:0  Rethrow as Exception: An exception has been thrown during the deserialization of an element of type GameLocationCharacterManager (serialization type: GameLocationSubmanager)   at BinarySerializer.SerializeElement[T] (System.String elementName, T value, Serializer+SerializationOption serializationOptions) [0x0045e] in <10624896cb4e451583b5b6d9ca571f3a>:0    at Serializer.SerializeElement[T] (System.String elementName, T value) [0x00000] in <10624896cb4e451583b5b6d9ca571f3a>:0    at GameDefinitions.SerializeManagerList[T] (IElementsSerializer serializer, System.Collections.Generic.List1[T] submanagerTypesCache, T[] submanagers, System.String[] legacySubmanagerTypes) [0x000dc] in <10624896cb4e451583b5b6d9ca571f3a>:0
at GameLocation.SerializeElements (IElementsSerializer serializer, IVersionProvider versionProvider) [0x00000] in <10624896cb4e451583b5b6d9ca571f3a>:0
at BinarySerializer.SerializeElement[T] (System.String elementName, T value, Serializer+SerializationOption serializationOptions) [0x00217] in <10624896cb4e451583b5b6d9ca571f3a>:0
Rethrow as Exception: An exception has been thrown during the deserialization of an element of type GameLocation (serialization type: GameLocation)
at BinarySerializer.SerializeElement[T] (System.String elementName, T value, Serializer+SerializationOption serializationOptions) [0x0045e] in <10624896cb4e451583b5b6d9ca571f3a>:0
at GameLocationManager.SerializeLocation (Serializer serializer) [0x00000] in <10624896cb4e451583b5b6d9ca571f3a>:0
at SessionState_LoadingSave.DeserializeLocation () [0x00028] in <10624896cb4e451583b5b6d9ca571f3a>:0
at SessionState_LoadingSave.LocationLoaded () [0x00045] in <10624896cb4e451583b5b6d9ca571f3a>:0
at (wrapper delegate-invoke) .invoke_void()
at GameLocationManager+d__152.MoveNext () [0x0060f] in <10624896cb4e451583b5b6d9ca571f3a>:0
at TA.Coroutine.Run () [0x00019] in <10624896cb4e451583b5b6d9ca571f3a>:0
UnityEngine.DebugLogHandler:Internal_LogException(Exception, Object)
UnityEngine.DebugLogHandler:LogException(Exception, Object)
UnityEngine.Logger:LogException(Exception, Object)
UnityEngine.Debug:LogException(Exception)
Trace:LogException(Exception)
TA.Coroutine:Run()
GameLocationManager:Update()
I loaded an older save and that started the game regularly.

Thanks for log but I still need your save before the crash.

Thanks for the quick reply! I managed to reproduce it. I was playing on the user created map "the Ultimate Dungeon", which is a popular map available through the Dungeon Maker.

Rename the file to .sav extension: Game crash paladin reaction.txt
Put friendlies within paladin aura, then use the "Guardian Aura" reaction (there's many reactions before "Guardian Aura" appears, ignore those. It crashes for me then with this error:

Uploading Crash Report
NullReferenceException: Object reference not set to an instance of an object
at SolastaUnfinishedBusiness.CustomDefinitions.FeatureDefinitionReduceDamage.DamageReduction (RulesetImplementationDefinitions+ApplyFormsParams formsParams, System.Int32 damage, System.String damageType) [0x00071] in <1b344617a2d5498d9035411730ab7648>:0
at SolastaUnfinishedBusiness.Patches.RulesetActorPatcher+InflictDamage_Patch.Prefix (System.Int32& rolledDamage, System.String damageType, RulesetImplementationDefinitions+ApplyFormsParams formsParams, RollInfo rollInfo) [0x00000] in <1b344617a2d5498d9035411730ab7648>:0
at (wrapper dynamic-method) RulesetActor.RulesetActor.InflictDamage_Patch1(int,DamageForm,string,RulesetImplementationDefinitions/ApplyFormsParams,RulesetActor,bool,ulong,bool,System.Collections.Generic.List`1,RollInfo,bool,bool&)
at SolastaUnfinishedBusiness.CustomBehaviors.GuardianAuraHpSwap+d__4.MoveNext () [0x0024d] in <1b344617a2d5498d9035411730ab7648>:0
at TA.Coroutine.Run () [0x00019] in <10624896cb4e451583b5b6d9ca571f3a>:0
UnityEngine.DebugLogHandler:Internal_LogException(Exception, Object)
UnityEngine.DebugLogHandler:LogException(Exception, Object)
UnityEngine.Logger:LogException(Exception, Object)
UnityEngine.Debug:LogException(Exception)
Trace:LogException(Exception)
TA.Coroutine:Run()
GameLocationActionManager:UpdateImpl()
GameLocationActionManager:Update()

that won't work. zip the save and attach.

Okay, I'll do that tomorrow. I'm on my phone, in bed now.

no worries. fixed.

Nice, well done!
Here's the zip if you'd still want it;
Game crash paladin reaction.zip

@ThyWoof do you have the commit or PR somewhere? I might contribute at some point.

I haven't used github collaberatively before


how to include com.google.ar.sceneform.ux:sceneform-ux:1.16.0 in build.gradle

Hi ,
I am trying to add sceneform-ux:1.16.0 in my build.gradle but it is not available in the gradle, Is this a deliberate decision where the core sceneform library is present in the gradle repository but for the ux lib  we have to download the source code and add it to our project.

As long as I know, you have to clone this repo and setup the settings.gradle to recognize the project, just like the sample.
And then in app/build.gradle you'll use implementation project('sceneformux') or implementation project('sceneform')

Yeah I did that but I was just thinking why have sceneform-core as a gradle library but not the sceneform ux, and updating the project whenever a new version arrives is quite wasteful, but thanks anyway

Starting in 1.16 Sceneform libraries are only available open source.  There is no longer a maven version.
Pre-1.15 the ux package was available on maven


trace.{}.Compose now can be called on nil

Pull request type

Please check the type of change your PR introduces:

[ ] Bugfix
[ ] Feature
[ ] Code style update (formatting, renaming)
[x] Refactoring (no functional changes, no api changes)
[ ] Build related changes
[ ] Documentation content changes
[ ] Other (please describe):

What is the current behavior?

Issue Number: N/A
What is the new behavior?

Other information

Codecov Report
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Patch %
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internal/cmd/gtrace/writer.go
0.00%
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2

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2

go-1.21.x
30
1

go-1.22.x
30
1

macOS
15
0

windows
15
0

ydb-23.3
15
0

integration
45
0

ydb-24.1
15
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ydb-24.2
15
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ydb-nightly
5
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experiment
5
0

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@@             Coverage Diff             @@
##           master    #1526       +/-   ##
===========================================
- Coverage   70.91%   41.02%   -29.90%
===========================================
  Files         356      353        -3
  Lines       37190    37298      +108
===========================================
- Hits        26373    15301    -11072
- Misses       9717    21489    +11772
+ Partials     1100      508      -592

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go-1.21.x
42.49% <ø> (-27.84%)
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go-1.22.x
41.01% <0.00%> (-27.35%)
:arrow_down:

go-1.23.x
?

integration
?

macOS
?

ubuntu
41.02% <0.00%> (-29.89%)
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unit
41.02% <0.00%> (+0.10%)
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ydb-23.3
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ydb-nightly
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How to capture a microphone?

Hello! Is there such an opportunity? How to do it?

@Seeman13 Audio is not supported, you can submit a PR to implement this.


feat: add isKeptAwake method

Closes #17
This PR implement isKeptAwake() method to check if the device is kept awake.
I also refactor some code in android by replacing Runnable with lambda expression.
Ideally, the code should be fairly concise:
    @PluginMethod
    public void keepAwake(final PluginCall call) {
        getBridge().executeOnMainThread(() -> {
            Window window = getActivity().getWindow();
            window.addFlags(WindowManager.LayoutParams.FLAG_KEEP_SCREEN_ON);
            call.resolve();
        });
    }

However, Prettier decided to go wild and add more indentation levels 😂
    @PluginMethod
    public void keepAwake(final PluginCall call) {
        getBridge()
            .executeOnMainThread(
                () -> {
                    Window window = getActivity().getWindow();
                    window.addFlags(WindowManager.LayoutParams.FLAG_KEEP_SCREEN_ON);
                    call.resolve();
                }
            );
    }

@robingenz is there any release date for this feature?


Login Items in Ventura

Hi,
Do you think if there is a way to grey out Nudge in LoginItems ? Since users can manage to disable Nudge from there ?
Note: we are managing Nudge using EMM Jamf Pro.
Thank you,

https://hammen.medium.com/managing-login-items-for-macos-ventura-e78d627f88b6


Added MOSS-I Report

Do not review and/or merge

Added MOSS-I output report.
Images in the image folder.
What's still missing:

One image (I've stuck in a placeholder, but the why OSS is important for universities one needs to go in there.)
Acknowledgements

Also need to check page breaks for printing

@Kevin-Mattheus-Moerman - cand you please review/merge and use this version for the next pdf test. Thanks a mil!

Thanks @claredillon. It's nearly there. It should work by Monday. Just wrangling the handling of references and a bibliography now.


Trouble with localStorage.getItem and 'hammerhead|storages-sandbox-temp'

Are you requesting a feature or reporting a bug?
A question, but I'd rather ask here unless it's forbidden to do so...
What is your Test Scenario?
Page checks for entry in localStorage -- if entry exists, redirect to different page after a number of seconds:
if (localStorage.getItem('project-saved-data')) {
      // Redirect user to /play page if save data is detected
      this.saveGameDetected = true;
      setTimeout(() => window.location.replace('/play'), 3000);
    }

What is the Current behavior?
The behaviour is as expected when not running through TestCafé, but within TestCafé, as the data is stored as 'hammerhead|storages-sandbox-temp', it doesn't trigger the expected behaviour.
What is the Expected behavior?
Page checks localStorage, sees that the particular entry exists and redirects the user after a number of seconds.
How would you reproduce the current behavior (if this is a bug)?
Write a test file with a ClientFunction that has localStorage.setItem() within it, then execute that function so it executes the localStorage.setItem() method. And then write an expect statement where the new post-redirection URL is expected to not be the same as the old pre-redirection URL.
Your complete test code (or attach your test files)
test('Save file exists: redirects to /play page', async t => {
  const getHref = ClientFunction(() => window.location.href);
  const saveToLS = ClientFunction(() => localStorage.setItem('project-saved-data', JSON.stringify({foo: bar})));

  await saveToLS();

  const oldUrl = await getHref();
  await t
    .wait(5000) // redirect action is carried out after 3 seconds -- this has an extra 2 seconds grace period

  const newUrl = await getHref();
  await t
    .expect(newUrl).notEql(oldUrl)
})

Your Environment details:

testcafe version:                   0.23.3
node.js version:                    10.13.0
command-line arguments:  testcafe firefox ./tests/e2e
browser name and version: Firefox 66.0.5
platform and version:          Windows 10
other:                                   -

How do I get the code to run as it does outside of TestCafé when the localStorage key is set differently?

Thank you for your inquiry. It looks very similar to DevExpress/testcafe-hammerhead#1999, so I close this issue as a duplicate. Please use it to get notifications about our progress in fixing the issue and check this comment for a workaround: AlexKamaev's comment.


Icon Button

I'm looking to create buttons in my application that do not contain text (only an icon).
Could we either create a new component (?) or make the text parameter of button optional and make it so the button is square around the icon (rather than taking up an extra space when an empty string is passed)?

https://github.com/xotahal/react-native-material-ui/blob/master/docs/IconToggle.md


Issue in fetching data.

Hi sir.First of all need to thank you for providing these codes.
I have been using it to fetch ledger wise vouchers from tally ERP 9.If the voucher number in tally is blank then the final data output comes as an error.
How to resolve?
Thanks in advance.

Hi Deppak
You should be capturing the Guid of the voucher to over come this issue.
Regards
Venugopal. G

Hi Deppak You should be capturing the Guid of the voucher to over come this issue. Regards Venugopal. G

Thank you sir.


[E 180118 17:30:13 base_handler:203] Cannot run the event loop while another loop is running     Traceback (most recent call last):

run a new project in console system ,follows show one message is below:
[E 180118 17:30:13 base_handler:203] Cannot run the event loop while another loop is running
Traceback (most recent call last):
how can i fix it, thank you !

i got the same problem ! ! ! Do you know how to solve it ? ? ?

I also have the same issue (WIN10 x64)
Main error when launching a project :
[E 180413 15:22:02 base_handler:203] Cannot run the event loop while another loop is running
    Traceback (most recent call last):
      File "c:\users\alex\appdata\local\programs\python\python36-32\lib\site-packages\pyspider\libs\base_handler.py", line 196, in run_task
        result = self._run_task(task, response)
      File "c:\users\alex\appdata\local\programs\python\python36-32\lib\site-packages\pyspider\libs\base_handler.py", line 175, in _run_task
        response.raise_for_status()
      File "c:\users\alex\appdata\local\programs\python\python36-32\lib\site-packages\pyspider\libs\response.py", line 172, in raise_for_status
        six.reraise(Exception, Exception(self.error), Traceback.from_string(self.traceback).as_traceback())
      File "c:\users\alex\appdata\local\programs\python\python36-32\lib\site-packages\six.py", line 692, in reraise
        raise value.with_traceback(tb)
      File "c:\users\alex\appdata\local\programs\python\python36-32\lib\site-packages\pyspider\fetcher\tornado_fetcher.py", line 143, in async_fetch
        result = yield self.http_fetch(url, task)
      File "c:\users\alex\appdata\local\programs\python\python36-32\lib\site-packages\tornado\gen.py", line 1099, in run
        value = future.result()
      File "c:\users\alex\appdata\local\programs\python\python36-32\lib\site-packages\tornado\gen.py", line 315, in wrapper
        yielded = next(result)
      File "c:\users\alex\appdata\local\programs\python\python36-32\lib\site-packages\pyspider\fetcher\tornado_fetcher.py", line 378, in http_fetch
        response = yield gen.maybe_future(self.http_client.fetch(request))
      File "c:\users\alex\appdata\local\programs\python\python36-32\lib\site-packages\tornado\httpclient.py", line 118, in fetch
        self._async_client.fetch, request, **kwargs))
      File "c:\users\alex\appdata\local\programs\python\python36-32\lib\site-packages\tornado\ioloop.py", line 576, in run_sync
        self.start()
      File "c:\users\alex\appdata\local\programs\python\python36-32\lib\site-packages\tornado\platform\asyncio.py", line 127, in start
        self.asyncio_loop.run_forever()
      File "c:\users\alex\appdata\local\programs\python\python36-32\lib\asyncio\base_events.py", line 412, in run_forever
        'Cannot run the event loop while another loop is running')
    Exception: Cannot run the event loop while another loop is running

Also have that Exception on pyspider startup :
Traceback (most recent call last):
  File "c:\users\alex\appdata\local\programs\python\python36-32\lib\threading.py", line 916, in _bootstrap_inner
    self.run()
  File "c:\users\alex\appdata\local\programs\python\python36-32\lib\threading.py", line 864, in run
    self._target(*self._args, **self._kwargs)
  File "c:\users\alex\appdata\local\programs\python\python36-32\lib\site-packages\pyspider\scheduler\scheduler.py", line 774, in xmlrpc_run
    import tornado.wsgi
  File "c:\users\alex\appdata\local\programs\python\python36-32\lib\site-packages\tornado\wsgi.py", line 86, in <module>
    _dummy_future = Future()
  File "c:\users\alex\appdata\local\programs\python\python36-32\lib\asyncio\events.py", line 694, in get_event_loop
    return get_event_loop_policy().get_event_loop()
  File "c:\users\alex\appdata\local\programs\python\python36-32\lib\asyncio\events.py", line 602, in get_event_loop
    % threading.current_thread().name)
RuntimeError: There is no current event loop in thread 'Thread-7'.```
The funny thing is my projects worked perfectly before I updated Pyspider...

same problem here. does anyone know how to fix it?

I solve this problem by:
pip install tornado==4.5


Update/null termination of values

*Added a function to create a null-terminated string from a charbuf
*Changed uriparser helper function to create charbuf instead of null-terminated strings
*Fixed bug for function to get key from server to work with PYKMIP
*Added comments to clarify code in key_table.c

This looks good, and I think it fully resolves issue #77.


ADNI exact data type used

Hi again,
Thanks again for looking into the issue I raised (#28).
I have already gained accessed to ADNI dataset, but I can only find .nii and .cdm data. As an example, a user you used based on your adni_dx_suvr_clean.csv is subject 21. When I look for the data of this person for T1 weigted MRI data I can only see files (in this case *.dcm) in a folder folder structure like:
./ADNI/011_S_0021/MPRAGE/2015-11-03_15_30_05.0/I543543/ADNI_011_S_0021_MR_MPRAGE_br_raw_20151105104743943_154_S299478_I543543.dcm
But in your adni_dataset.py the folder structure is mentioned as name: mri/grey/white/pet:
https://github.com/VITA-Group/Self-PU/blob/a0e332ae4f8110e2490d597876e36bf837e1060f/adni_dataset.py#L146
Also I don't really see which data format of the images are you using in adni_dataset.py? is it DCM (.dcm)? is it NIfTI (nii)?
To me it seems like you have did some preprocessing on images and store them as .npy but I don't know where to find the code for that preprocessing. Do you mind sharing that please?
Another confusion I have is that why the default folder is mentioned as name: mri/grey/white/pet? I thought MRI images are being used and not PET images?
Thank you!

Hi naji-s,
Thanks again for your interest.
As we have mentioned in Issue #5, our dataset was downloaded and pre-processed by a company. Therefore, a lot of details are under NDA agreement. I am willing to help with anything else but I do feel sorry since we cannot reveal those details. Would you mind running experiments with a customized setting that anything you can set up on our side? Please let me know if your have further questions.

Hi naji-s,
I will try to see what I can do from my side - I am afraid that I can no longer share any related data or scripts but please feel free to ask questions. I would try my best to engage in discussion too if time permitted.


CSV printer

in .stages

SHould use a dependency: https://github.com/melrief/PureCSV
Not adding it now. Closing until then


Table: Action - AddKey

Similar to FunctionCall, let's make a table for the Action Event AddKey.
My proposed schema is:

[ ] action_id
[ ] tx_hash
[ ] block_timestamp
[ ] nonce
[ ] public_key
[ ] permission
[ ] allowance
[ ] method_name
[ ] receiver_id

There are two structures here. When a user selects FullAccess, there are no necessary arguments.
{
  "access_key": {
    "nonce": 0,
    "permission": "FullAccess"
  },
  "public_key": "ed25519:5Ejo1izVBqUsHJPpGmBSSQ5ZPYoCejw2cEw2Cn7AMV1"
}

However, if a user selects specific methods that may be called by the contract, then the permissions object has the following structure:
  "FunctionCall": {
    "allowance": "250000000000000000000000",
    "method_names": [
      "add_request",
      "add_request_and_confirm",
      "delete_request",
      "confirm"
    ],
    "receiver_id": "forrest68.near"
  }
}

I think we should keep all AddKey actions together, but should we parse the more complex permissions or leave as JSON? If parsed, those columns would be NULL for when permissions = FullAccess
cc: @chuxinh

Branch created with model for the AddKey action

If the permisson object has very similar structure, I think it's better just to parse them with a note in documentation that it'd be NULL for full access

Yes, it looks like the same structure whenever permission is not FullAccess. Ok, I will move forward with this approach. Thanks

Model available for review, linking PR momentarily.
root@6b6d8a5cf473:/near# dbt run -m actions_events_addkey
Running with dbt=0.21.1
Found 7 models, 61 tests, 0 snapshots, 0 analyses, 175 macros, 0 operations, 0 seed files, 2 sources, 0 exposures

23:49:16 | Concurrency: 4 threads (target='dev')
23:49:16 |
23:49:16 | 1 of 1 START incremental model DEV.actions_events_addkey............. [RUN]
23:49:22 | 1 of 1 OK created incremental model DEV.actions_events_addkey........ [SUCCESS 1 in 5.46s]
23:49:22 |
23:49:22 | Finished running 1 incremental model in 11.98s.

Completed successfully

Done. PASS=1 WARN=0 ERROR=0 SKIP=0 TOTAL=1


Fix for #126 as initially proposed by @bbrangeo; pushing for speed (since i need it.. :) )

Description
Fixes #126 with changes proposed by @bbrangeo
Related Issue
Fixes #126
Example

Tested locally:
Python 3.10.12 (main, Jun 11 2023, 05:26:28) [GCC 11.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pygbif
>>>

Thanks @CecSve !

Sorry to ask here, but does anyone happen to know when the update will be released to make new installations work?

@airnst Not sure, but if you are blocked you can install from source with pip:
pip install git+https://github.com/gbif/pygbif.git@master

i think that should work...

I am not sure but I think this fix raised a new problem see #145
The specific error line was one introduced in this fix.
If I downgrade to pygbif==0.6.3 it fixes #145

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Project coverage is 80.17%. Comparing base (59960ff) to head (c8e4c8d).
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pygbif/caching.py
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##           master     #127      +/-   ##
==========================================
+ Coverage   80.00%   80.17%   +0.17%
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  Files          26       26
  Lines         675      671       -4
==========================================
- Hits          540      538       -2
+ Misses        135      133       -2

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VM service broken in profile mode

Steps to reproduce as of https://github.com/flutter/flutter/commit/ed6e7fa06f85ff6c3a66a5d0ab69aad70a5da506:

flutter run --profile
open observatory in the browser

Another way to reproduce is:

flutter run --profile --trace-startup

A log message "Ignoring error posting over WebSocket." is printed that seems to be coming from this line
/cc @turnidge @rmacnak-google

@rmacnak-google - Could this be related to the recent work you've done on websocket:

This is a bug in the flutter build. https://github.com/flutter/flutter/issues/5627


Add Title Option

Adding a 'title' option.

Would be easier to review in 2 different PRs, one for formatting, the other about title :)


page not found in Android Simulator Fluttter APP with static folder

Hi, I try to run the get_server in a flutter app on Android Simulator,
I can return a Text('Hello') , but when I set a static folder, the page not found.
home: FolderWidget('web') // not found the folder

runApp(GetServer(
host: '<IP_ADDRESS>',
port: 8088,
home: FolderWidget('web', allowDirectoryListing:true),
getPages: [
GetPage(name: '/hello',  page:()=>Text('Hello')),
],
));

I know the reason now.
That is because the flutter code can not find the folder, You can create a folder in getApplicationDocumentsDirectory and copy files into the above folder and then FolderWidget(the full folder above)

Glad you found the solution. Based on your comment, I'm closing this


UI_Canvas causes lag when childed to gameobject

Hi, I'm new to VR and vrtk has been a great tool to learn how interactions works. I'm using version 3.1.0 in unity 5.6, using vive atc and SteamVR
At the moment I've added an in-game tablet to act as an info page, with buttons as widgets to open different sliders. So I've added a world canvas as a child of a 3d gameobject however when I activate the VRTK_UI_Canvas script it makes the games extremely laggy when I look at the object. Also the mesh freezes in place while the canvas can be moved around or lags behind it, with the script disabled the objects can be moved normally
I've resorted to deactivate the main script and manually add the components. It works fine for the sliders but I can't press buttons, I'm assuming other interactions are also disabled. I'm trying to think of a workaround with other scripts or just write something myself, but I would like to understand what's the issue here
should I invert the parenting?

Check your console. If there's something getting logged repeatedly this will take down the fps a ton. If there's nothing in the console use the profile to figure out what actually takes all the time during play.
Additionally you'll have to come up with steps for us to reproduce your issue in one of the example scenes since your description doesn't explain that. The ISSUE_TEMPLATE that GitHub pasted into the text area when you opened this issue and you just removed and didn't bother to use is mandatory (as is said on that document).

Also, if you're using version 3.1.0 (from the Unity asset store) then it's not compatible with Unity 5.6

I though I was clear. I've added a gameobject with childed custom meshes, and a world canvas copied from vrtk, the canvas with a few buttons. With the standard unity scripts the canvas works fine but enabling VRTK_UI Canvas makes the game lag when the headset look at the object.
Aside from that the room is a single mesh with an area light and ref. probe. There were some vrtk canvases active already and it worked fine so far. Figured it was incompatability, it keeps reapeating Invalid AABB bug

@Belial0331 where did you get your version of VRTK from? The unity asset store?

originally yes

Originally? So where is it from now?

tryed the github version but was giving me errors of missing methods or cloned classes, so I was still in the one from the store
found the issue tho, forgot to clean up some files while trying to switch versions, seems to be working ok now
sorry for wasting your time


Add testing API for py-shiny

Hi!
Right now, it's very hard to test the shiny part of your dashboard.
While the internals of py-shiny are tested with playwright, the testing API with ShinyAppProc and more is not in the package.
I'm keeping my fingers crossed for a quick release of shiny.testing namespace as it would allow us creating testable (i.e. enterprise ready) shiny apps in python, just like in R. :)
Any ideas when to expect this feature?
Correct me if I'm wrong, but there's no issue on GH that tracks the progress of testing namespace, hence I created this one.

Relevant links:

Discord thread
Discord #testing channel
Example of simple ui test
Example of simple server test

Hi @pstorozenko 👋 !
@karangattu and I are aiming for a testing release near conf in the early fall.  We are hoping to have the existing classes (and their methods) documented and moved under shiny.test (or something similar).

It seems reasonable to try to make basic testing possible in the near future (knowing the API might change), such as the simple UI test linked above. (Functions related to conftest)
The other helper controls could be aded piecemeal as we document / vet them.

Great to hear that!
In the meantime, I'm working on the blog post on how to test pyshiny apps with playwright right now, will share here and on discord once it's ready:)

For all those wanting to test your apps right now
It's great that there's an Epic for testing shiny apps 🎉
In the meantime you can check this repo with examples.
And the accompanying blog post.
For adding tests to the CI/CD pipeline you can use this snippet in conftest.py (check this SO thread).
This assumes the app is defined as app = App(...) in the app.py file.
import threading

import pytest
import requests
from tenacity import retry, stop_after_delay, wait_fixed
from uvicorn import Config, Server

APP_HOST = "<IP_ADDRESS>"
APP_PORT = 8989
APP_URL = f"http://{APP_HOST}:{APP_PORT}"

@retry(wait=wait_fixed(0.5), stop=stop_after_delay(10))
def wait_for_server_to_start(url):
    response = requests.get(url)  # noqa: S113
    response.raise_for_status()  # Will raise an exception if the request is unsuccessful, i.e. server is not ready

def run_server():
    config = Config(app="app:app", host=APP_HOST, port=APP_PORT, log_level="info")
    server = Server(config)
    server.run()

@pytest.fixture(scope="session", autouse=True)
def _shiny_server():
    # Start the server in a background thread
    thread = threading.Thread(target=run_server, daemon=True)
    thread.start()

    wait_for_server_to_start(APP_URL)

    return


Fix deprecated-mage-check task parameters

What does this PR do?
Screenshot/screencast of this PR

What issues does this PR fix or reference?

How to test this PR?

quay.io/redhat-appstudio/pull-request-builds:spi-controller-#
quay.io/redhat-appstudio/pull-request-builds:spi-oauth-#

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

Project coverage is 71.65%. Comparing base (70369e5) to head (44821b0).
Report is 23 commits behind head on main.

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #956      +/-   ##
==========================================
+ Coverage   69.87%   71.65%   +1.78%
==========================================
  Files          94       93       -1
  Lines        6087     4774    -1313
==========================================
- Hits         4253     3421     -832
+ Misses       1465      991     -474
+ Partials      369      362       -7

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


fix: invalid composer command when app reloaded

bugs runtime/container folder doesn't removed when hot reload triggered

Cannot delete runtime/container folder, because watcher need rewrite one proxy class file not all the proxy classes.


[BUG] - SHFQA multiplexed readout : incommensurate integration weights.

Describe the bug
The weights queried from the SHFQA using a node query do not correspond one-to one with weights uploaded by the user (i.e. to the compiled experiment).
To Reproduce
Steps to reproduce the behavior:

Consider the experiment.json & setup.json, it is 2 qubit on-off experiment. The two measure & acquire tones are ~1 GHz apart, essentially -500 MHz and 500 MHz, from the LO at 6.5 GHz.
The compiled experiment reports the correct weights, but when queried from the device, strange clipping is shown. The FFT of the weights reports a frequency that differs from supplied (SW oscillator) frequency by >10 MHz.
Device nodes queried:
weights:
daq.get(f'/dev12159/qachannels/{port}/readout/integration/weights/0/wave', flat=True)[f'/dev12159/qachannels/{port}/readout/integration/weights/0/wave'][0]['vector']
daq.get(f'/dev12159/qachannels/{port}/readout/integration/weights/1/wave', flat=True)[f'/dev12159/qachannels/{port}/readout/integration/weights/1/wave'][0]['vector']

measurement pulse:
daq.get('/dev12159/qachannels/0/generator/waveforms/0/wave', flat=True)['/dev12159/qachannels/0/generator/waveforms/0/wave'][0]['vector']
daq.get('/dev12159/qachannels/0/generator/waveforms/1/wave', flat=True)['/dev12159/qachannels/0/generator/waveforms/1/wave'][0]['vector']

The multiplexed readout thus performed, shows a significant degradation of fidelity, which we attribute to partially incorrect weights.

Expected behavior
The queried weights should be almost the same as the one uploaded. The degradation seen in readout fidelity should be smaller.
Versions used:
Version laboneq 1.0.2, Labone 22.08, zhinst : 21.2.15439
Context
experiment_setup_zipped.zip

[ ] No workaround known. Degrades readout fidelity.
[ ] Yes, however the first demonstration of multiplexed readout was successful.

This issue is related to #1, especially step 2 from the description has the same root cause:

The compiled experiment reports the correct weights, but when queried from the device, strange clipping is shown.

It is not clear yet, if the read-out fidelity degradation is also caused by this. In case the root issue only affects the node readout, then the degraded fidelity must have a different cause. Otherwise, if corrupted weights are seen by the integrators same as on the node readout, this would explain degraded fidelity too.

Hi, the bug is due to a current issue in LabOne 22.08 which is being addressed in the upcoming patch release. As Konstantin stated, it is not yet clear if the fidelity issue is related, though it is likely an due to LabOne and not LabOne Q. We will be able to test this one our side shortly after internal testing of the 22.08 patch. At the moment, the readout weight uploaded to the device is correct, however, daq.get doesn't retrieve it correctly, resulting in your reported behavior. We should have an update to this issue shortly.

It is already known, that only the weight node read out from the device was affected, not the actual data used for integration. This means degraded fidelity must have a different source.

This issue should be fixed with the new LabOne firmware, which LabOne Q will now depend on. When installing LabOne Q, make sure to also update the firmware on your instruments through the LabOne GUI.
Closing this issue.


Prepended require throws error

I'm currently replacing a project's gulp build with 100% webpack.
Within the project the riot tag files get compiled individually so the generated JS files can be included individually.
<script src="tags/tag1.js"></script>
<script>
  riot.mount('*');
</script>

So far this has been done with gulp-riot that internally uses riot.
With my webpack build the head of each file looks different and contains
var riot = require('riot')

This throws an error: Uncaught ReferenceError: require is not defined
I've found out this gets prepended to the outout within the tag-loader.
I guess it's needed for some use cases (as you probably wouldn't have added it otherwise) but for me it's breaking my code.
Would it be ok to add an option to disable this so I get only the compiled code?
Apart from that I've found out that the gulp-riot plugin introduced a custom option (I'm using) which also prepends code to the output:
if (options.modular) {
  compiledCode = `(function(tagger) {\n  if (typeof define === 'function' && define.amd) {\n    define(['riot'], function(riot) { tagger(riot); });\n  } else if (typeof module !== 'undefined' && typeof module.exports !== 'undefined') {\n    tagger(require('riot'));\n  } else {\n    tagger(window.riot);\n  }\n})(function(riot) {\n${compiledCode}\n\n});`;
}

Hence same question here:
would a be ok to add the same option (modular) to the loader?

This example is also webpack 100% and works without any problem https://github.com/riot/examples/tree/gh-pages/webpack . Your problem is probably somewhere else

@GianlucaGuarini your linked example is using a deprecated version of webpack:
loaders and preloaders don't get defined like that anymore!
Would you please explain to me why the var riot = require('riot') gets prepended by the loader?
Maybe this helps me to understand the issue better.
However I'm afraid it's simply my way of individually including the precompiled tag files (see my HTML example above) that explains why I'm having a problem with the loader.

https://github.com/riot/examples/blob/gh-pages/webpack/package.json#L26

Ok, I see the code / config has been updated accordingly. But I would recommend to update the README as well because it's still showing the deprecated setup.
However this doesn't solve my problem because I've a similar webpack config.
As I said the prepended require() of the loader is the reason for my problem.
I've added an additional option to disable it which fixes the issue.
I'll submit a PR later so you can see what I mean.
p.s.
I would recommend to replace query with options in your linked webpack example because query is deprecated (even if still supported)
https://webpack.js.org/configuration/module/#rule-options-rule-query

Rule.query is deprecated in favor of Rule.options and UseEntry.options.

closing this issue more info


bcbio_setup_genome.py: error while running prepare_tx_gff.py

Hi all,
I am trying to generate files for E. coli MG1655 to run the RNAseq pipeline. This might be related to Issue  #1608:
cd ~

FASTA=/ginkgo/bitome/users/lina/references/genomes/ecoli_mg1655.fa
ANNOTATION=/ginkgo/bitome/users/lina/references/genomes/ecoli_mg1655.gtf
NAME=ecoli_mg1655
BUILD=ecoli_mg1655_build

~/local/bin/bcbio_setup_genome.py -f $FASTA -g $ANNOTATION -i bowtie2 star seq bwa -n $NAME -b $BUILD &> ecoli_mg1655.log

The log output with error messages is pasted here:
cat ecoli_mg1655.log

...

[2016-10-26 11:31:49] Beginning TopHat run (v2.0.10)
-----------------------------------------------
[2016-10-26 11:31:49] Checking for Bowtie
  Bowtie 2 not found, checking for older version..
          Bowtie version:    <IP_ADDRESS>
[2016-10-26 11:31:50] Checking for Samtools
        Samtools version:    <IP_ADDRESS>
[2016-10-26 11:31:50] Checking for Bowtie index files (genome)..
Error: Could not find Bowtie index files (/home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/bowtie2/ecoli_mg1655_build.*.ebwt)
Creating gffutils database for /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/tmpcbl/ref-transcripts.gtf.
Writing out merged GTF file to /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/tmpcbl/ref-transcripts.gtf.
Creating gffutils database for /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/tmpcbl/rRNA.gtf.
Traceback (most recent call last):
  File "/home/lina/cloudbiolinux/utils/prepare_tx_gff.py", line 821, in <module>
    main(args.org_build, args.gtf, args.fasta, genome_dir, args.cores)
  File "/home/lina/cloudbiolinux/utils/prepare_tx_gff.py", line 297, in main
    prepare_tophat_index(gtf_file, org_build, genome_fasta)
  File "/home/lina/cloudbiolinux/utils/prepare_tx_gff.py", line 504, in prepare_tophat_index
    subprocess.check_call(cmd.format(**locals()), shell=True)
  File "/home/lina/local/share/bcbio/anaconda/lib/python2.7/subprocess.py", line 541, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'tophat --transcriptome-index /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/tmpcbl/tophat/ecoli_mg1655_build_transcriptome -G /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/tmpcbl/ref-transcripts.gtf -o /tmp/tmpWuzMSd /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/bowtie2/ecoli_mg1655_build dummy.fq' returned non-zero exit status 1
Creating directories using /home/lina/local/share/bcbio/genomes as the base.
Genomes will be installed into /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build.
Installed genome as /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/seq/ecoli_mg1655_build.fa.
Installed GTF as /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/rnaseq/ref-transcripts.gtf.
Creating the bowtie2 index.
[localhost] local: mkdir /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/seq/../bowtie2
[localhost] local: ln -sf ../seq/ecoli_mg1655_build.fa /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/bowtie2/ecoli_mg1655_build.fa
Creating the star index.
[localhost] local: mkdir /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/star
Creating the seq index.
[localhost] local: samtools faidx ecoli_mg1655_build.fa
[localhost] local: picard -Xms500m -Xmx3500m CreateSequenceDictionary REFERENCE=/home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/seq/ecoli_mg1655_build.fa OUTPUT=/home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/seq/ecoli_mg1655_build.dict
Creating the bwa index.
[localhost] local: mkdir bwa
[localhost] local: ln -sf /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/seq/ecoli_mg1655_build.fa
[localhost] local: bwa index -a bwtsw ecoli_mg1655_build.fa
[localhost] local: rm -f ecoli_mg1655_build.fa
Traceback (most recent call last):
  File "/home/lina/local/bin/bcbio_setup_genome.py", line 4, in <module>
    __import__('pkg_resources').run_script('bcbio-nextgen==0.9.9', 'bcbio_setup_genome.py')
  File "/home/lina/local/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/__init__.py", line 726, in run_script
  File "/home/lina/local/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/__init__.py", line 1484, in run_script
  File "/home/lina/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.9-py2.7.egg-info/scripts/bcbio_setup_genome.py", line 277, in <module>
    subprocess.check_call(cmd.format(**locals()), shell=True)
  File "/home/lina/local/share/bcbio/anaconda/lib/python2.7/subprocess.py", line 541, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '/home/lina/local/share/bcbio/anaconda/bin/python /home/lina/cloudbiolinux/utils/prepare_tx_gff.py --cores 1 --genome-dir /home/lina/local/share/bcbio/genomes --gtf /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/rnaseq/ref-transcripts.gtf ecoli_mg1655 ecoli_mg1655_build' returned non-zero exit status 1

First, I actually have bowtie2 installed:
lina@compute1:~$ which bowtie2
/usr/bin/bowtie2

lina@compute1:~$ bowtie2 --version
/usr/bin/bowtie2-align-s version 2.2.4
64-bit
Built on sputnik
Sun Oct 26 07:21:16 UTC 2014
Compiler: gcc version 4.9.1 (Debian 4.9.1-19)
Options: -O3 -m64 -msse2  -funroll-loops -g3 -Wl,-z,relro
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}

But later in the log file, it says Creating the bowtie2 index. I assume this might be a hard-coded message (?).
It looks like the prepare_tx_gff.py script contains a lot of hard-coded builds for non-microbial organisms. Is it appropriate for organisms that are not in the UCSC browser?
Thanks for any advice!
~Lina

Hi,
sorry about this.
sometimes automatizing the indexing of these genomes bring some problems.
Can you go to this folder: /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/tmpcbl/
what do you have there and are they empty?
right now I am not sure why tophat2 and bowtie2 are failing. Are tophat2 and bowite2 installed in the same place? not sure if this is even important.

On Oct 26, 2016, at 11:50 AM, lfaller<EMAIL_ADDRESS>wrote:
Hi all,
I am trying to generate files for E. coli MG1655 to run the RNAseq pipeline:
cd ~
FASTA=/ginkgo/bitome/users/lina/references/genomes/ecoli_mg1655.fa
ANNOTATION=/ginkgo/bitome/users/lina/references/genomes/ecoli_mg1655.gtf
NAME=ecoli_mg1655
BUILD=ecoli_mg1655_build
~/local/bin/bcbio_setup_genome.py -f $FASTA -g $ANNOTATION -i bowtie2 star seq bwa -n $NAME -b $BUILD &> ecoli_mg1655.log
The log output with error messages is pasted here:
cat ecoli_mg1655.log
...
[2016-10-26 11:31:49] Beginning TopHat run (v2.0.10)
[2016-10-26 11:31:49] Checking for Bowtie
Bowtie 2 not found, checking for older version..
Bowtie version:    <IP_ADDRESS>
[2016-10-26 11:31:50] Checking for Samtools
Samtools version:    <IP_ADDRESS>
[2016-10-26 11:31:50] Checking for Bowtie index files (genome)..
Error: Could not find Bowtie index files (/home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/bowtie2/ecoli_mg1655_build.*.ebwt)
Creating gffutils database for /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/tmpcbl/ref-transcripts.gtf.
Writing out merged GTF file to /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/tmpcbl/ref-transcripts.gtf.
Creating gffutils database for /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/tmpcbl/rRNA.gtf.
Traceback (most recent call last):
File "/home/lina/cloudbiolinux/utils/prepare_tx_gff.py", line 821, in
main(args.org_build, args.gtf, args.fasta, genome_dir, args.cores)
File "/home/lina/cloudbiolinux/utils/prepare_tx_gff.py", line 297, in main
prepare_tophat_index(gtf_file, org_build, genome_fasta)
File "/home/lina/cloudbiolinux/utils/prepare_tx_gff.py", line 504, in prepare_tophat_index
subprocess.check_call(cmd.format(**locals()), shell=True)
File "/home/lina/local/share/bcbio/anaconda/lib/python2.7/subprocess.py", line 541, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'tophat --transcriptome-index /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/tmpcbl/tophat/ecoli_mg1655_build_transcriptome -G /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/tmpcbl/ref-transcripts.gtf -o /tmp/tmpWuzMSd /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/bowtie2/ecoli_mg1655_build dummy.fq' returned non-zero exit status 1
Creating directories using /home/lina/local/share/bcbio/genomes as the base.
Genomes will be installed into /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build.
Installed genome as /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/seq/ecoli_mg1655_build.fa.
Installed GTF as /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/rnaseq/ref-transcripts.gtf.
Creating the bowtie2 index.
[localhost] local: mkdir /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/seq/../bowtie2
[localhost] local: ln -sf ../seq/ecoli_mg1655_build.fa /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/bowtie2/ecoli_mg1655_build.fa
Creating the star index.
[localhost] local: mkdir /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/star
Creating the seq index.
[localhost] local: samtools faidx ecoli_mg1655_build.fa
[localhost] local: picard -Xms500m -Xmx3500m CreateSequenceDictionary REFERENCE=/home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/seq/ecoli_mg1655_build.fa OUTPUT=/home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/seq/ecoli_mg1655_build.dict
Creating the bwa index.
[localhost] local: mkdir bwa
[localhost] local: ln -sf /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/seq/ecoli_mg1655_build.fa
[localhost] local: bwa index -a bwtsw ecoli_mg1655_build.fa
[localhost] local: rm -f ecoli_mg1655_build.fa
Traceback (most recent call last):
File "/home/lina/local/bin/bcbio_setup_genome.py", line 4, in
import('pkg_resources').run_script('bcbio-nextgen==0.9.9', 'bcbio_setup_genome.py')
File "/home/lina/local/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/init.py", line 726, in run_script
File "/home/lina/local/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/init.py", line 1484, in run_script
File "/home/lina/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.9-py2.7.egg-info/scripts/bcbio_setup_genome.py", line 277, in
subprocess.check_call(cmd.format(**locals()), shell=True)
File "/home/lina/local/share/bcbio/anaconda/lib/python2.7/subprocess.py", line 541, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '/home/lina/local/share/bcbio/anaconda/bin/python /home/lina/cloudbiolinux/utils/prepare_tx_gff.py --cores 1 --genome-dir /home/lina/local/share/bcbio/genomes --gtf /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/rnaseq/ref-transcripts.gtf ecoli_mg1655 ecoli_mg1655_build' returned non-zero exit status 1
First, I actually have bowtie2 installed:
lina@compute1:~$ which bowtie2
/usr/bin/bowtie2
lina@compute1:~$ bowtie2 --version
/usr/bin/bowtie2-align-s version 2.2.4
64-bit
Built on sputnik
Sun Oct 26 07:21:16 UTC 2014
Compiler: gcc version 4.9.1 (Debian 4.9.1-19)
Options: -O3 -m64 -msse2  -funroll-loops -g3 -Wl,-z,relro
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
But later in the log file, it says Creating the bowtie2 index. I assume this might be a hard-coded message (?).
It looks like the prepare_tx_gff.py script contains a lot of hard-coded builds for non-microbial organisms. Is it appropriate for organisms that are not in the UCSC browser?
Thanks for any advice!
~Lina
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I am reading this better, and it says is not finding bowtie2 indexes, not bowtie2 right?. But the bowtie2 is created after that.
Anyway, did you tried to re-start, just using the same bcbio command and see if you get exactly the same?
let me know if you have the bowtie2 index folder, and if re-starting gives a different error?

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Hi Lorena,
I checked, and I don't have this folder:
$ pwd
/home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/bowtie2

$ ls -lah
total 15M
drwxr-xr-x 2 lina ginkgo 4.0K Oct 26 11:31 .
drwxr-xr-x 8 lina ginkgo 4.0K Oct 26 11:31 ..
-rw-r--r-- 1 lina ginkgo 5.5M Oct 26 11:31 ecoli_mg1655_build.1.bt2
-rw-r--r-- 1 lina ginkgo 1.2M Oct 26 11:31 ecoli_mg1655_build.2.bt2
-rw-r--r-- 1 lina ginkgo   17 Oct 26 11:31 ecoli_mg1655_build.3.bt2
-rw-r--r-- 1 lina ginkgo 1.2M Oct 26 11:31 ecoli_mg1655_build.4.bt2
lrwxrwxrwx 1 lina ginkgo   28 Oct 26 11:31 ecoli_mg1655_build.fa -> ../seq/ecoli_mg1655_build.fa
-rw-r--r-- 1 lina ginkgo 5.5M Oct 26 11:31 ecoli_mg1655_build.rev.1.bt2
-rw-r--r-- 1 lina ginkgo 1.2M Oct 26 11:31 ecoli_mg1655_build.rev.2.bt2

I can create it, if that helps. Is it supposed to contain the bowtie2 indexes?
I ran the same command two more times, but I still get the same error message as before:
[2016-10-27 11:47:21] Beginning TopHat run (v2.0.10)
-----------------------------------------------
[2016-10-27 11:47:21] Checking for Bowtie
  Bowtie 2 not found, checking for older version..
		  Bowtie version:	 <IP_ADDRESS>
[2016-10-27 11:47:21] Checking for Samtools
		Samtools version:	 <IP_ADDRESS>
[2016-10-27 11:47:21] Checking for Bowtie index files (genome)..
Error: Could not find Bowtie index files (/home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/bowtie2/ecoli_mg1655_build.*.ebwt)
Writing out merged GTF file to /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/tmpcbl/ref-transcripts.gtf.
Traceback (most recent call last):
  File "/home/lina/cloudbiolinux/utils/prepare_tx_gff.py", line 821, in <module>
    main(args.org_build, args.gtf, args.fasta, genome_dir, args.cores)
  File "/home/lina/cloudbiolinux/utils/prepare_tx_gff.py", line 297, in main
    prepare_tophat_index(gtf_file, org_build, genome_fasta)
  File "/home/lina/cloudbiolinux/utils/prepare_tx_gff.py", line 504, in prepare_tophat_index
    subprocess.check_call(cmd.format(**locals()), shell=True)
  File "/home/lina/local/share/bcbio/anaconda/lib/python2.7/subprocess.py", line 541, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'tophat --transcriptome-index /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/tmpcbl/tophat/ecoli_mg1655_build_transcriptome -G /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/tmpcbl/ref-transcripts.gtf -o /tmp/tmp1p_L6I /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/bowtie2/ecoli_mg1655_build dummy.fq' returned non-zero exit status 1
Creating directories using /home/lina/local/share/bcbio/genomes as the base.
Genomes will be installed into /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build.
Installed genome as /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/seq/ecoli_mg1655_build.fa.
Installed GTF as /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/rnaseq/ref-transcripts.gtf.
Creating the bowtie2 index.
Creating the star index.
Creating the seq index.
Creating the bwa index.
Traceback (most recent call last):
  File "/home/lina/local/bin/bcbio_setup_genome.py", line 4, in <module>
    __import__('pkg_resources').run_script('bcbio-nextgen==0.9.9', 'bcbio_setup_genome.py')
  File "/home/lina/local/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/__init__.py", line 726, in run_script
  File "/home/lina/local/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/__init__.py", line 1484, in run_script
  File "/home/lina/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.9-py2.7.egg-info/scripts/bcbio_setup_genome.py", line 277, in <module>
    subprocess.check_call(cmd.format(**locals()), shell=True)
  File "/home/lina/local/share/bcbio/anaconda/lib/python2.7/subprocess.py", line 541, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '/home/lina/local/share/bcbio/anaconda/bin/python /home/lina/cloudbiolinux/utils/prepare_tx_gff.py --cores 1 --genome-dir /home/lina/local/share/bcbio/genomes --gtf /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/rnaseq/ref-transcripts.gtf ecoli_mg1655 ecoli_mg1655_build' returned non-zero exit status 1

I also tried running the offending command on its own:
$ tophat --transcriptome-index /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/tmpcbl/tophat/ecoli_mg1655_build_transcriptome -G /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/tmpcbl/ref-transcripts.gtf -o /tmp/tmp1p_L6I /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/bowtie2/ecoli_mg1655_build dummy.fq

[2016-10-27 11:48:06] Beginning TopHat run (v2.0.10)
-----------------------------------------------
[2016-10-27 11:48:06] Checking for Bowtie
  Bowtie 2 not found, checking for older version..
Error: Bowtie not found on this system.

$ which bowtie
$ which bowtie2
/usr/bin/bowtie2

If possible, I assume I should be using bowtie2. Is there a reason why it wouldn't find bowtie2 even though it's in my path?
Thanks for your help!

ok, I will try to replicate this.
Any way you can send me the FASTA and GTF file to me?
thanks!

On Oct 27, 2016, at 11:50 AM, lfaller<EMAIL_ADDRESS>wrote:
Hi Lorena,
I checked, and I don't have this folder:
$ pwd
/home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/bowtie2
$ ls -lah
total 15M
drwxr-xr-x 2 lina ginkgo 4.0K Oct 26 11:31 .
drwxr-xr-x 8 lina ginkgo 4.0K Oct 26 11:31 ..
-rw-r--r-- 1 lina ginkgo 5.5M Oct 26 11:31 ecoli_mg1655_build.1.bt2
-rw-r--r-- 1 lina ginkgo 1.2M Oct 26 11:31 ecoli_mg1655_build.2.bt2
-rw-r--r-- 1 lina ginkgo   17 Oct 26 11:31 ecoli_mg1655_build.3.bt2
-rw-r--r-- 1 lina ginkgo 1.2M Oct 26 11:31 ecoli_mg1655_build.4.bt2
lrwxrwxrwx 1 lina ginkgo   28 Oct 26 11:31 ecoli_mg1655_build.fa -> ../seq/ecoli_mg1655_build.fa
-rw-r--r-- 1 lina ginkgo 5.5M Oct 26 11:31 ecoli_mg1655_build.rev.1.bt2
-rw-r--r-- 1 lina ginkgo 1.2M Oct 26 11:31 ecoli_mg1655_build.rev.2.bt2
I can create it, if that helps. Is it supposed to contain the bowtie2 indexes?
I ran the same command two more times, but I still get the same error message as before:
[2016-10-27 11:47:21] Beginning TopHat run (v2.0.10)
[2016-10-27 11:47:21] Checking for Bowtie
Bowtie 2 not found, checking for older version..
Bowtie version:    <IP_ADDRESS>
[2016-10-27 11:47:21] Checking for Samtools
Samtools version:    <IP_ADDRESS>
[2016-10-27 11:47:21] Checking for Bowtie index files (genome)..
Error: Could not find Bowtie index files (/home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/bowtie2/ecoli_mg1655_build.*.ebwt)
Writing out merged GTF file to /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/tmpcbl/ref-transcripts.gtf.
Traceback (most recent call last):
File "/home/lina/cloudbiolinux/utils/prepare_tx_gff.py", line 821, in
main(args.org_build, args.gtf, args.fasta, genome_dir, args.cores)
File "/home/lina/cloudbiolinux/utils/prepare_tx_gff.py", line 297, in main
prepare_tophat_index(gtf_file, org_build, genome_fasta)
File "/home/lina/cloudbiolinux/utils/prepare_tx_gff.py", line 504, in prepare_tophat_index
subprocess.check_call(cmd.format(**locals()), shell=True)
File "/home/lina/local/share/bcbio/anaconda/lib/python2.7/subprocess.py", line 541, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'tophat --transcriptome-index /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/tmpcbl/tophat/ecoli_mg1655_build_transcriptome -G /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/tmpcbl/ref-transcripts.gtf -o /tmp/tmp1p_L6I /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/bowtie2/ecoli_mg1655_build dummy.fq' returned non-zero exit status 1
Creating directories using /home/lina/local/share/bcbio/genomes as the base.
Genomes will be installed into /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build.
Installed genome as /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/seq/ecoli_mg1655_build.fa.
Installed GTF as /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/rnaseq/ref-transcripts.gtf.
Creating the bowtie2 index.
Creating the star index.
Creating the seq index.
Creating the bwa index.
Traceback (most recent call last):
File "/home/lina/local/bin/bcbio_setup_genome.py", line 4, in
import('pkg_resources').run_script('bcbio-nextgen==0.9.9', 'bcbio_setup_genome.py')
File "/home/lina/local/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/init.py", line 726, in run_script
File "/home/lina/local/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/init.py", line 1484, in run_script
File "/home/lina/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.9-py2.7.egg-info/scripts/bcbio_setup_genome.py", line 277, in
subprocess.check_call(cmd.format(**locals()), shell=True)
File "/home/lina/local/share/bcbio/anaconda/lib/python2.7/subprocess.py", line 541, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '/home/lina/local/share/bcbio/anaconda/bin/python /home/lina/cloudbiolinux/utils/prepare_tx_gff.py --cores 1 --genome-dir /home/lina/local/share/bcbio/genomes --gtf /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/rnaseq/ref-transcripts.gtf ecoli_mg1655 ecoli_mg1655_build' returned non-zero exit status 1
I also tried running the offending command on its own:
$ tophat --transcriptome-index /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/tmpcbl/tophat/ecoli_mg1655_build_transcriptome -G /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/tmpcbl/ref-transcripts.gtf -o /tmp/tmp1p_L6I /home/lina/local/share/bcbio/genomes/ecoli_mg1655/ecoli_mg1655_build/bowtie2/ecoli_mg1655_build dummy.fq
[2016-10-27 11:48:06] Beginning TopHat run (v2.0.10)
[2016-10-27 11:48:06] Checking for Bowtie
Bowtie 2 not found, checking for older version..
Error: Bowtie not found on this system.
$ which bowtie
$ which bowtie2
/usr/bin/bowtie2
If possible, I assume I should be using bowtie2. Is there a reason why it wouldn't find bowtie2 even though it's in my path?
Thanks for your help!
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I will -- thanks for helping look into this!
Link to dropbox: https://www.dropbox.com/sh/dw88466sp055r6d/AACs75EbsmxAq0-mUDxKwQcIa?dl=0
Let me know if that works :)

Hi,
I  cannot replicate this, so I am guessing the problem is missing bowtie2 for some reason, even if it is there.
Are tophat2 or bowti2 binary the ones installed by bcbio? if yes, I have not many more ideas for now. But will try to go further tomorrow.
sorry, my week was epic and couldn't do this early.

No worries and thanks for looking into this for me!
I noticed that there is another version of bowtie2 installed. The one that's on my PATH is v 2.2.4 and the other one is 2.2.8 and I think that one was installed by bcbio. I will try to figure out if the newer one works. Otherwise I'll start fresh.

Hi @lfaller
I will close this guessing it worked at the end. Let us know if you find more issues. I hope it worked at the end.


runtime-proxy: extract annotations from labels for docker

Ⅰ. Describe what this PR does
runtime-proxy: extract annotations from labels for docker
In dockershim，annotations and labels are merged because docker supports only labels.
We should extract annotations from labels for docker in failOver as we do in HandleCreateContainer of RuntimeManagerDockerServer.
Ⅱ. Does this pull request fix one issue?
None
Ⅲ. Describe how to verify it
Ⅳ. Special notes for reviews
V. Checklist

[x] I have written necessary docs and comments
[x] I have added necessary unit tests and integration tests
[x] All checks passed in make test

Why do you need to do this, can you add some description to help everyone understand its purpose?

In dockershim，annotations and labels are merged because docker supports only labels.
We should extract annotations from labels for docker in failOver as we do in HandleCreateContainer of RuntimeManagerDockerServer.
You can look this

I got it, thanks for contributing this pr.

/LGTM


Minimal local CI for Meltano GUI

Migrated from GitLab: https://gitlab.com/meltano/meltano/-/issues/112
Originally created by @joshlambert on 2018-10-04 17:37:31

Overview
A first time user should be able to use Meltano to get data from A to B within 5 minutes.
Once users find value, they can explore doing more advanced things, such as DAG's and distributed execution of jobs. But for the simple first use case of a single data source, it should be dead simple.
It's also likely that for narrower use cases, a large percentage of users may not need these advanced features.
Hypothesis
I believe we have two general personas:

Business or analytics users who are looking for the path of least resistance to accomplish the task at hand. Perhaps getting data out of SFDC, mix with Marketo, and run a report.
Data teams who are looking for a complete ELT solution, with both data engineers, scientists, or analysts on staff.

We can serve both of these needs, with a crawl walk run.
Proposal
Build a minimal, super simple CI capability into Meltano. It would be able to locally:

Execute docker run to kick off a job (just like the runner would)
Run docker logs to display job status
Pass secrets as environment variables on docker run command  (just like the runner would)
Simple 2-stage pipeline per source: Extract/Load -> Transform
Simple cron for scheduling

This should be relatively low effort, require few if any additional dependencies, and provide a super simple and fast getting started experience. It will even likely address a healthy % of use cases.
For any more advanced use cases, require the setup/integration with GitLab CI. But at least they could kick the tires, prove it works, without going through all the integration work first.
Appendix: Integration with GitLab CI effort/requirements
When evaluatingGitLab CI, it has become clear that integration will be:

High effort

Need to generate the pipeline definition
Execute the pipeline
Display overall pipeline status
Display job log / status
Surface errors
Manage secrets
Manage schedule

Require extra setup

GitLab runner, even in the upcoming local mode, still requires the GitLab server
Requiring at minimum an account on GitLab.com, or an entire server
Synchronization of the .gitlab-ci.yml

View 14 previous comments from the original issue on GitLab


is there any way to have the game window displayed.

when running test:
python experiment.py --mode=test --level_name=dmlab30 --dataset_path=/home/rjn/projects/RL/dataset/ --test_num_episodes=10
is there any way to have the game window displayed.

You would need to dump the frames either in PyProcessDmLab or in the agent somewhere.

I was able to do this by passing in a visibility flag :
 enviroments.py
  def step(self, action):
    if self.visable:
       cv2.imshow("xxxxxx",observation[0])
       cv2.waitKey(1)
and to
    experiment.py
       env = create_environment(level_name, seed=i + 1, visable=(i==0))

this can also be passed on the call to test.

cv2.imshow("xxxxxx",observation[0])
cv2.waitKey(1)

Have you tried any other visualization methods?
@rnunziata

cv2.imshow("xxxxxx",observation[0])
cv2.waitKey(1)

Have you tried any other visualization methods?
@rnunziata


Jumpstart quickstart has invalid configuration

Description
I am working on some small fixes to our service's migration script to bring in all quickstarts to our database. Our service handles validation on all raw configuration for alerts and dashboards as well.
I'm running into errors importing a particular quickstart into the system, the Jumpstart quickstart. It's got some invalid alert configuration preventing me from importing it because it uses a union for all of the enum fields.
For example, I see baselineDirection set to this: LOWER_ONLY | UPPER_AND_LOWER | UPPER_ONLY. This is invalid because it must be 1 of those values, but not all 3. This is true for any of the fields that have that union operator in this alert configuration.
I do see this quickstart included in public I/O and the product. Looking further at it, it looks like its supposed to serve as an example for other quickstarts to follow, which is nice, but we currently have no way of making this distinction in the system. This is problematic because if a user actually thinks this is a valid quickstart and goes to try and install this quickstart, it will quickly fail as the alert configuration is totally invalid.
My question is: Do we even want this in I/O to begin with? Seems like it might be better moved elsewhere in this repo to serve as a template for other quickstarts, but its not a great quickstart itself.
If the intention is to keep it, then we are going to need some special logic to flag this as an example and provide some UX around this so that we don't allow a user to get partway through a quickstart install only for it to fail. If I were a user, I'd walk away unimpressed as to why the demo quickstart was unable to be successfully installed.
I could ignore this quickstart during the migration, but this will only last until someone changes it again. As soon as that example quickstart is updated, it will be marked invalid and will not be allowed to be merged. I'd love to discuss further how we should handle this as this is problematic.

@jcountsNR 👋


Move to latest Java release (21)

Only Oracle released 21 officially for now, so let's wait for OpenJDK to come out with their version to relaunch the CI here