python: rename block types

https://github.com/iotaledger/iota-sdk/issues/1515

Still need to do the block header change.

Closed by https://github.com/iotaledger/iota-sdk/pull/1774


setup.exe wont run

Hi
The extracted Setup.exe will not run.

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

ID: 6a003f6a-2edb-3303-01c1-41a63ce82260
Version Independent ID: 203d6b80-acd5-566a-3f6c-be1852ae8909
Content: Deploy Office 365 ProPlus as part of an operating system image
Content Source: DeployOffice/deploy-office-365-proplus-as-part-of-an-operating-system-image.md
Service: o365-proplus-itpro
GitHub Login: @DHB-MSFT
Microsoft Alias: danbrown

Do you get an error message? What are you typing at the command line when running setup.exe?


Transaction message check back

The issue tracker is ONLY used for bug report and feature request. Keep in mind, please check whether there is an existing same report before your raise a new one.
Alternately (especially if your communication is not a bug report), you can send mail to our mailing lists. We welcome any friendly suggestions, bug fixes, collaboration and other improvements.
Please ensure that your bug report is clear and that it is complete. Otherwise, we may be unable to understand it or to reproduce it, either of which would prevent us from fixing the bug. We strongly recommend the report(bug report or feature request) could include some hints as the following:
BUG REPORT

Please describe the issue you observed:
In TransactionalMessageBridge.getMessage method,
when store return status is OFFSET_OVERFLOW_ONE, PullStatus.OFFSET_ILLEGAL will be set to PullResult, so, in TransactionServiceImpl.fillOpRemoveMap method, the code as follows will be execute:
transactionalMessageBridge.updateConsumeOffset(opQueue, pullResult.getNextBeginOffset());
this will result opQueueOffset error.

What did you do (The steps to reproduce)?

What did you expect to see?
I think should set the PullStatus.NO_NEW_MSG to PullResult in this TransactionalMessageBridge.getMessage method, because of it's no offset overflow,
just like the process method of PullMessageProcessor.

What did you see instead?

Please tell us about your environment:
Local mac pro

Other information (e.g. detailed explanation, logs, related issues, suggestions how to fix, etc):

FEATURE REQUEST

Please describe the feature you are requesting.

Provide any additional detail on your proposed use case for this feature.

Indicate the importance of this issue to you (blocker, must-have, should-have, nice-to-have). Are you currently using any workarounds to address this issue?

If there are some sub-tasks using -[] for each subtask and create a corresponding issue to map to the sub task:

sub-task1-issue-number: sub-task1 description here,
sub-task2-issue-number: sub-task2 description here,
...

I think you are right, set PullStatus.NO_NEW_MSG in this situation is better.

You are right, set PullStatus.NO_NEW_MSG in this situation is better.
But I think set PullStatus.OFFSET_ILLEGAL is also ok. If store#getMessage return OFFSET_OVERFLOW_ONE, the value of pullResult.getNextBeginOffset() is equal to the query offset. So transactionalMessageBridge#updateConsumeOffset just reset the same value, this will not cause offset error.

You are right, set PullStatus.NO_NEW_MSG in this situation is better.
But I think set PullStatus.OFFSET_ILLEGAL is also ok. If store#getMessage return OFFSET_OVERFLOW_ONE, the value of pullResult.getNextBeginOffset() is equal to the query offset. So transactionalMessageBridge#updateConsumeOffset just reset the same value, this will not cause offset error.

Yeah, you are right, no serious consequences found at present.


Explanation for the auth middleware ?

First of all thanks for an amazing repo. It is one of the most useful repos out there for express.
I was going through the structure of it and the only thing I couldn't completely understand was the flow of auth middleware with respect to user roles.
This part basically.
This is the link to the whole file.
  const logIn = Promise.promisify(req.logIn);
  const apiError = new APIError({
    message: error ? error.message : 'Unauthorized',
    status: httpStatus.UNAUTHORIZED,
    stack: error ? error.stack : undefined,
  });

  try {
    if (error || !user) throw error;
    await logIn(user, { session: false });
  } catch (e) {
    return next(apiError);
  }

  if (roles === LOGGED_USER) {
    if (user.role !== 'admin' && req.params.userId !== user._id.toString()) {
      apiError.status = httpStatus.FORBIDDEN;
      apiError.message = 'Forbidden';
      return next(apiError);
    }
  } else if (!roles.includes(user.role)) {
    apiError.status = httpStatus.FORBIDDEN;
    apiError.message = 'Forbidden';
    return next(apiError);
  } else if (err || !user) {
    return next(apiError);
  }

  req.user = user;

Thank you, @tusharf5!
The purpose of this middleware is to check if the user has the role that you specified in the router file.
The logic of the LOGGED_USER is weird, my programming skills wasn't that good back then, sorry about that. But I will try to explain what I did:
If the user is an admin, then he can access everything, if he is not an admin then the param of the url should contain his id, so he can't access other users info.
In production I recommend you to use a known and tested library to handle the authorization part of the api, maybe one of those should help you:
https://www.npmjs.com/package/accesscontrol
https://www.npmjs.com/package/express-jwt-permissions
https://www.npmjs.com/package/connect-roles

@danielfsousa Thanks for replying. We're using an implementation of access control that is very tightly coupled with our business Logic (which I think is not good :D ). I'll surely submit a PR if we come up with a more generic solution since we partially used your repository as the base of our app 👍 .


xen: fix seabios path

Description of changes

Things done

Built on platform(s)

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

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

[ ] sandbox = relaxed
[x] 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/)
24.11 Release Notes (or backporting 23.11 and 24.05 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.

Ideally we'd have something similar to OVMF.firmware. @AndersonTorres as the SeaBIOS maintainer, would you be opposed to a passthru.firmware attribute that pointed to ${finalAttrs.finalPackage}/share/seabios/${firmware} where firmware is Csm16.bin by default?

Also, I'm assuming #341429 will need to override seabios to point to qubes-seabios?

Yes, that's right. qubes-seabios is packaged in qubes-packages PR, wanted firmware filename is "bios-256k.bin"

Yes, that's right. qubes-seabios is packaged in qubes-packages PR, wanted firmware filename is "bios-256k.bin"

Add something like this to qubes-seabios:
passthru.firmware = "${finalAttrs.finalPackage}/share/seabios/bios-256k.bin";

and once we get the firmware attr in the main seabios package, it'll Just Work™ and is cleaner than another override.

To me, no problems. I am working on this:
https://github.com/NixOS/nixpkgs/pull/342692


Grid decimal seperator

Grid decimal seperator is "." dot. Can it take from system setting for other cultures ?

I would like that very much, too.

@Jdochoa this is a nice feature, but breaks compatibility with "COPY AS INSERT/UPDATE"
I'll suggest to rollback for now because this breaks current behavior with the iteration with Firebird itself when I change a value directly from the grid (update)

@Jdochoa I'll comment this line:
https://github.com/mariuz/flamerobin/blob/f909af0786116f5d871c1c6138b4226b71affbc6/src/main.cpp#L84
and generate a new snapshot, ok?

OK
./jo

@Jdochoa I downloaded and tried this option, but looks like location is always enabled checking or not the checkbox at Preferences my grid has ',' (comma) instead of '.' (dot)
By the way my locale is indeed ',' (comma) but I prefer using dot 😸

@Jdochoa I downloaded and tried this option, but looks like location is always enabled checking or not the checkbox at Preferences my grid has ',' (comma) instead of '.' (dot)
By the way my locale is indeed ',' (comma) but I prefer using dot 😸

@Jdochoa I downloaded and tried this option, but looks like location is always enabled checking or not the checkbox at Preferences my grid has ',' (comma) instead of '.' (dot)
By the way my locale is indeed ',' (comma) but I prefer using dot 😸

Hi @arvanus
I can't reproduce it.
you have more information?
The next snapshot depend of this.
Thank you.
./jo

Hello @Jdochoa!
So, I unchecked this option and the grid keep using comma, just after I closed and reopened completely Fr that if worked OK
I think that just putting a label informing the need to restart is enough!
Something like this:

I found the "problem"
https://github.com/mariuz/flamerobin/blob/4f17dc5b88e09fc7bc460ae1647af153b37e2eb8/src/config/Config.cpp#L409
default should be "false"
I'll change it right here and commit
For now, it's good enough to the snapshot!

Or... change here to true:
https://github.com/mariuz/flamerobin/blob/4f17dc5b88e09fc7bc460ae1647af153b37e2eb8/conf-defs/fr_settings.confdef#L15
You decide @Jdochoa :)

@arvanus  i committed two changes:

Change default to "False"
Reload configuration to save changes to settings.

With this, please generate a new snapshot.
./jo

Nice!
please pull request :)

Perfect! :D
I'll edit What's New in the docs and generate a snapshot

New snapshot available!
https://github.com/mariuz/flamerobin/releases/tag/<IP_ADDRESS>
@Zeki-Gursoy can you try this snapshot and close this issue?
@Jdochoa you are awesome :)
Thanks!

Perfect for pasting into Excel and exporting to CSV.
@Jdochoa, Thank you very much ;)

@Jdochoa
when I try to update a integer value, I'm getting this error here:

Here:
https://github.com/mariuz/flamerobin/blob/d4a6eae13a7b04803cb08c3acb1789c55cd0de8f/src/gui/controls/DataGridRows.cpp#L558-L559
Debugging, the string comes as "1.0000" instead of simply '1'
This error occurs since snapshot 8


#76 - EO up to 0.24.0

@rultor merge

@rultor merge

@graur OK, I'll try to merge now. You can check the progress of the merge here


Remove HelChartInstall CRD

Due to operator's permissions, the declarative approach would be
complicated. We are replacing the HelmChartInstall by an imperative
request.

Cc @rawagner


Run_digits not working

I tried your example in run digits but It doesn't work.
The error is this:
Traceback (most recent call last):
File "run_digits.py", line 223, in
main(data_prefix, output_prefix, gamma, m, alltestm, kernel_type, do_output_pics)
File "run_digits.py", line 187, in main
os.path.join(data_prefix, 'usps.t'))
File "run_digits.py", line 116, in run
plotfigs2(digitsdat.X[selected[sortedindx], :], selectedy[sortedindx], outfig)
File "run_digits.py", line 67, in plotfigs2
ax = fig.add_subplot(gs[i - begin_at])
File "/usr/local/lib/python3.6/dist-packages/matplotlib/figure.py", line 1419, in add_subplot
a = subplot_class_factory(projection_class)(self, *args, **kwargs)
File "/usr/local/lib/python3.6/dist-packages/matplotlib/axes/_subplots.py", line 73, in init
self.update_params()
File "/usr/local/lib/python3.6/dist-packages/matplotlib/axes/_subplots.py", line 133, in update_params
return_all=True)
File "/usr/local/lib/python3.6/dist-packages/matplotlib/gridspec.py", line 592, in get_position
rows, cols = np.unravel_index([self.num1, self.num2], (nrows, ncols))
File "<array_function internals>", line 6, in unravel_index
TypeError: 'float' object cannot be interpreted as an integer
I fixed the problem by modifying the run_digits.py in line 54 by added int before the nrows and ncolumns  arguments of GridSpec:
gs = gridspec.GridSpec(int(int(perpic_m/perrow)+offset/perrow), int(perrow), wspace=0.0, hspace=0.0)
Hope this is useful for someone.

@francescobodria Yes it's really helpful! Thanks a lot for ur post!

I tried your example in run digits but It doesn't work.
The error is this:
Traceback (most recent call last):
File "run_digits.py", line 223, in
main(data_prefix, output_prefix, gamma, m, alltestm, kernel_type, do_output_pics)
File "run_digits.py", line 187, in main
os.path.join(data_prefix, 'usps.t'))
File "run_digits.py", line 116, in run
plotfigs2(digitsdat.X[selected[sortedindx], :], selectedy[sortedindx], outfig)
File "run_digits.py", line 67, in plotfigs2
ax = fig.add_subplot(gs[i - begin_at])
File "/usr/local/lib/python3.6/dist-packages/matplotlib/figure.py", line 1419, in add_subplot
a = subplot_class_factory(projection_class)(self, *args, **kwargs)
File "/usr/local/lib/python3.6/dist-packages/matplotlib/axes/_subplots.py", line 73, in init
self.update_params()
File "/usr/local/lib/python3.6/dist-packages/matplotlib/axes/_subplots.py", line 133, in update_params
return_all=True)
File "/usr/local/lib/python3.6/dist-packages/matplotlib/gridspec.py", line 592, in get_position
rows, cols = np.unravel_index([self.num1, self.num2], (nrows, ncols))
File "<array_function internals>", line 6, in unravel_index
TypeError: 'float' object cannot be interpreted as an integer
I fixed the problem by modifying the run_digits.py in line 54 by added int before the nrows and ncolumns arguments of GridSpec:
gs = gridspec.GridSpec(int(int(perpic_m/perrow)+offset/perrow), int(perrow), wspace=0.0, hspace=0.0)
Hope this is useful for someone.


Throttle read RPC

There's throttling options available for bulk mutation RPC. Are there any plans for implementing a throttle option for reading? If there are none - how much of an effort would it be for someone else, like myself, to implement the feature?

What's the use case you had in mind for reading?
Some background:
Bulk mutations have an application in batch jobs.  Batch write jobs are really efficient and can easily push a Cloud Bigtable Cluster to its limit.  Writes also are "unary RPCs" with a single request / response model, so there was a place where the client could measure the health of the service by measuring RPC response times; that "measure of health" is used to slow down RPCs if the service responds slowly.
Cloud Bigtable is really efficient at reading sequential rows, and it's difficult to bring down a service with a batch job that reads an entire table.  Reads are "streaming RPCs", and there isn't a simple way to get a proxy for service health like there is with Writes.

Thanks for the background.
We use dataflow jobs to read from BT at scale and we sometimes face issues with BT not being able to auto-scale fast enough to keep up with the auto-scaling dataflow jobs, causing them to stop (a theory we have). One idea we had was to implement throttling in the dataflow job but I wanted to start here to see if I could learn more.
Does that answer your question? Thanks.

@simeg did you figure out any solution? We face the same problem, cloud dataflow can very well bringdown a bigtable cluster with its table scans. What I've been doing is to limit auto scaling in dataflow to a lowerbound which won't break our bigtable cluster but that's annoying since after we read rows from bigtable we can use way more nodes and our job takes more than it should since we can't increase the limit afterwards. I described the situation here too:  https://stackoverflow.com/questions/58565633/dynamically-scale-cloud-dataflow-job?noredirect=1#comment103500714_58565633 but no solution.

@bshafiee No we did not come up with a good solution. We've also tweaked dataflow (limit the amount of threads for example) and tweaked auto-scaling settings for BigTable. We still have this issue.

Dataflow reading from Bigtable appears to quickly push Bigtable CPU usage over 90%. We're looking for a solution to throttle dataflow streaming reads


Automated cherry pick of #2060: support get model distinct field

Cherry pick of #2060 on release/2.10.0.
#2060: support get model distinct field

Codecov Report

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The diff coverage is 0%.

@@               Coverage Diff                @@
##             release/2.10.0   #2062   +/-   ##
================================================
  Coverage                  ?   7.58%
================================================
  Files                     ?     410
  Lines                     ?   63309
  Branches                  ?       0
================================================
  Hits                      ?    4802
  Misses                    ?   58095
  Partials                  ?     412

Flag
Coverage Δ

#aFlag
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Impacted Files
Coverage Δ

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[Enhancement] disable aws sdk curl init

curl init is already done alone in starrocks_main

Fixes #issue
What type of PR is this:

[ ] BugFix
[ ] Feature
[X] Enhancement
[ ] Refactor
[ ] UT
[ ] Doc
[ ] Tool

Does this PR entail a change in behavior?

[ ] Yes, this PR will result in a change in behavior.
[X] No, this PR will not result in a change in behavior.

If yes, please specify the type of change:

[ ] Interface/UI changes: syntax, type conversion, expression evaluation, display information
[ ] Parameter changes: default values, similar parameters but with different default values
[ ] Policy changes: use new policy to replace old one, functionality automatically enabled
[ ] Feature removed
[ ] Miscellaneous: upgrade & downgrade compatibility, etc.

Checklist:

[ ] I have added test cases for my bug fix or my new feature
[ ] This pr needs user documentation (for new or modified features or behaviors)

[ ] I have added documentation for my new feature or new function

Bugfix cherry-pick branch check:

[X] I have checked the version labels which the pr will be auto-backported to the target branch

[X] 3.2
[ ] 3.1
[ ] 3.0
[ ] 2.5

[FE Incremental Coverage Report]
:heart_eyes: pass : 0 / 0 (0%)

@Mergifyio backport branch-3.2

[BE Incremental Coverage Report]
:heart_eyes: pass : 0 / 0 (0%)


[FLOC-4411] Use the latest version of oauth2client

Fixes: https://clusterhq.atlassian.net/browse/FLOC-4411
Our update-requirements tool dragged in a few other dependencies that have been updated since last week  when we last ran the tool.

I merged this forward and re-ran the tests.
All passed except a flaky client installation test.
Merging.


Language level inconsistency between jsonnet and ksonnet

Is this a BUG REPORT or FEATURE REQUEST?:

Uncomment only one, leave it on its own line:

/kind bug

/kind feature

What happened:
When merging two objects the behavior is different across jsonnet and ksonnet in the case where the key of an object is specified as a variable as opposed to a literal.
What you expected to happen:
Both jsonnet and ksonnet show the same results when merging objects.
How to reproduce it (as minimally and precisely as possible):
I will add a detailed, minimal test case as the first comment in this issue.
Anything else we need to know?:
Does not work on ks 0.13 and 0.12 (does work correctly on ks 0.9).
Environment:

ksonnet version (use ks version):
Kubernetes version (use kubectl version):
ksonnet version: 0.13.1
jsonnet version: v0.11.2
client-go version: kubernetes-1.10.4
(kubectl is irrelevant since this is a manifestation bug)

No, adding or removing spaces does not change the behavior


@Data creates private default constructor if there are any other constructors

@Data
public class Parent {
  private String s;

  public Parent(String s) {
    this.s = s;
  }
}

In the above example I cannot use
Parent p= new Parent();
because the generated default constructor's visibility is private.
If there is no manually created constructor then the visibility of the default constructor is public, as it's expected.

Add @NoArgsConstructor before @Data to have public default one.

Add @NoArgsConstructor before @Data to have public default one.

Yep. That works, as a quick fix, thank you.
But I still believe that the order of the annotations shouldn't affect their behaviour.

What version are you using?

No response from reporter
Why we closed this issue


build(mikro-orm): bump mikro-orm from 5.4.2 to 5.9.8

closes #2640
relates-to: mikro-orm/mikro-orm#3992

Summary by CodeRabbit

Chores

Updated ORM package versions to enhance database interaction stability and performance.

Tests

Modified integration tests to support replica set configurations, ensuring more robust testing scenarios.

:tada: This PR is included in version 7.67.7 :tada:
The release is available on:

v7.67.7
GitHub release

Your semantic-release bot :package::rocket:


Sorting is not working

grid = $("#viewGrid1").grid({
//selectionType: "multiple",
//selectionMethod: "checkbox",
autoLoad: false, //absolutely necessary!
loadonce:true,
uiLibrary: "bootstrap",
dataSource: { url: '/RepairOrderViews/GetRepairOrderByStatus', data: { statusCode: 'E' } },
defaultColumnSettings: { headerCssClass: "bootstrapgridoverride center", sortable: true},
//Non-Worked Repair Orders
columns: [
{ field: "RepairOrderNumber", name: "RO", title: "RO", align: "right", },
{ field: "RepairOrderStatusDesc", title: "Status", type: "string"},

I'm not able to replicate this issue with your code sample. Can you see requests to the backend with correct sortBy and direction parameters, when you click on a column header?
What is the version of the grid that you are using?

What are the parameters I am supposed to be using, I didn't see any in the help pages?
Thanks for your help.Matt
  From: Atanas Atanasov<EMAIL_ADDRESS>
To: atatanasov/gijgo<EMAIL_ADDRESS>Cc: mbutler71<EMAIL_ADDRESS>Sent: Saturday, March 5, 2016 10:26 AM
Subject: Re: [gijgo] Sorting is not working (#6)
I'm not able to replicate this issue with your code sample. Can you see requests to the backend with correct sortBy and direction parameters, when you click on a column header?
What is the version of the grid that you are using?—
Reply to this email directly or view it on GitHub.
Sent from Yahoo Mail      From: Atanas Atanasov<EMAIL_ADDRESS>To: atatanasov/gijgo<EMAIL_ADDRESS>Cc: mbutler71<EMAIL_ADDRESS>Sent: Saturday, March 5, 2016 10:26 AM
Subject: Re: [gijgo] Sorting is not working (#6)
I'm not able to replicate this issue with your code sample. Can you see requests to the backend with correct sortBy and direction parameters, when you click on a column header?
What is the version of the grid that you are using?—
Reply to this email directly or view it on GitHub.

I see in the Google debugger the parameters to send for sorting and paging... page-limit-sortBy-direction.
Thanks.

Matt,
You can change the parameter name with the following configuration options if needed:
http://gijgo.com/Grid/Configuration/defaultParams.sortBy
http://gijgo.com/Grid/Configuration/defaultParams.direction
http://gijgo.com/Grid/Configuration/defaultParams.limit
http://gijgo.com/Grid/Configuration/defaultParams.page

Great. Thanks for your help.


[access log] handle empty string in formatter

Signed-off-by: Asra Ali<EMAIL_ADDRESS>Commit Message: If a struct formatter is configured with an empty string, then we crash on this ASSERT that has an assumption that parse always adds a formatter. Parsing does not add any formatters on an empty string, so handle that case. https://github.com/envoyproxy/envoy/blob/3f740bc90d32ac442e70da46ebf4d03a1bdb479d/source/common/formatter/substitution_formatter.cc#L215
Risk Level: Low, configuration issue only.
Testing: Added unit tests for struct formatter, parse, and local_reply_integration_test, as well as fuzzer regression testcase
Fixes
https://bugs.chromium.org/p/oss-fuzz/issues/detail?id=29752&sort=-opened&can=1&q=proj%3Aenvoy status%3DNew
Alternatively I could have removed that ASSERT and returned ValueUtil::stringValue("") from the callback if there were no providers, but that is what this does too at a lower level. It also doesn't seem right to treat the value as DefaultUnspecifiedValueString, since it's not looking for a value.

Alternatively I could have removed that ASSERT and returned ValueUtil::stringValue("") from the callback if there were no providers, but that is what this does too at a lower level. It also doesn't seem right to treat the value as DefaultUnspecifiedValueString, since it's not looking for a value.

I think you picked a better approach -- it's more readable/maintainable as there's no special "provider-less" case for empty strings buried in StructFormatter::providersCallback call.


Use OpenZeppelin ERC20 Contracts

We should swap out our use of the Consensys EIP20 contracts for the OpenZeppelin ERC20 contracts. The latter contracts have been audited more and are the current community gold standard.

done


Update aws-java-sdk-cloudwatch, ... to 1.11.996

Updates

com.amazonaws:aws-java-sdk-cloudwatch
com.amazonaws:aws-java-sdk-dynamodb
com.amazonaws:aws-java-sdk-kinesis

from 1.11.728 to 1.11.996.
I'll automatically update this PR to resolve conflicts as long as you don't change it yourself.
If you'd like to skip this version, you can just close this PR. If you have any feedback, just mention me in the comments below.
Configure Scala Steward for your repository with a .scala-steward.conf file.
Have a fantastic day writing Scala!

Ignore future updates
Add this to your .scala-steward.conf file to ignore future updates of this dependency:
updates.ignore = [ { groupId = "com.amazonaws" } ]

labels: library-update, semver-patch

Superseded by #24.


Development

Also, @Chris-Mugumwa you should enter in VS Code, press Control+shift+P, search Settings UI and search for Indentation. You should select this to true

We should do this because when I save a SCSS file, even though I modify only one line, all the tabs are transformed into spaces.

@Chris-Mugumwa Can you please create a task for adding the Poppins font family to placeholders?

@Chris-Mugumwa I will close this PR in order to deploy the website to our competition. You will be still able to watch the closed PR


Installation problem

Hello,
I just try to install the plugin, but I get some error.
I install it via composer, activate the plugin, but when i click install in the extension panel, I get error in the response request:

Strict Standards:  Non-static method Participation\Plugin::createDocuments() should not be called
 statically in www\plugins\Participation\lib\Participation\Plugin.php on line 76

Strict Standards:  Non-static method Participation\Plugin::createDocumentTypes() should not be
 called statically in www\plugins\Participation\lib\Participation\Plugin
.php on line 77

Strict Standards:  Non-static method Participation\Plugin::createEmailDocuments() should not be
 called statically in www\plugins\Participation\lib\Participation\Plugin
.php on line 78

{"message":"Error: Unable to create email document page [\/participation-confirmation]: ParentID and
 ID is identical, an element can't be the parent of itself.","reload":false,"status":{"installed":false
},"success":true}

Test was done on the last stable Pimcore (4.4.1, build 4008), Windows server.
Thanks.

Ok I fixed all the error by adding static keyword to the function:
private static function createDocuments()
private static function createDocumentTypes()
private static function createEmailDocuments()
private static function createConfigFile()
And by changing in plugin.php, line 246 (https://github.com/basilicom/pimcore-plugin-participation/blob/master/lib/Participation/Plugin.php#L246):
Page::getByPath(dirname(self::DOCUMENT_EMAIL_CONFIRMATION_PATH))
By:
Page::getByPath(str_replace("\\", "/", dirname(self::DOCUMENT_EMAIL_CONFIRMATION_PATH)))
After this, install work ok, and all necessary things are created.
If you could add those change to the plugin so next user on Windows and with Strict level won't have any problem this would be great.
Thanks a lot!

hi!
your feedback is highly appreciated, I'll definitely take a look at it
tomorrow!
Kind regards, Chris
Am 22.11.2016 7:27 Nachm. schrieb "Yivan"<EMAIL_ADDRESS>Ok I fixed all the error by adding static keyword to the function:
private static function createDocuments()
private static function createDocumentTypes()
private static function createEmailDocuments()
private static function createConfigFile()
And by changing in plugin.php, line 246 (https://github.com/basilicom/
pimcore-plugin-participation/blob/master/lib/Participation/Plugin.php#L246):
Page::getByPath(dirname(self::DOCUMENT_EMAIL_CONFIRMATION_PATH))
By:
Page::getByPath(str_replace("\", "/", dirname(self::DOCUMENT_EMAIL_
CONFIRMATION_PATH)))
After this, install work ok, and all necessary things are created.
If you could add those change to the plugin so next user on Windows and
with Strict level won't have any problem this would be great.
Thanks a lot!
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Default snap icon should be 1:1 square

The icon is not an exact square.

We can close this right? We removed the icon entirely @FrederikBolding right?

We haven't yet, but we will in https://github.com/MetaMask/template-snap-monorepo/pull/138.
Closing.


etcd3: include GroupResource in logs/metrics

Update kube to pull in https://github.com/kcp-dev/kubernetes/pull/95
Use GroupResource instead of object reflection when recording the
following metrics:

etcd_request_duration_seconds
etcd_bookmark_counts

Add GroupResource to logs and traces where only reflection-based typing
was previously used.
Both of these changes allow us to disginguish between different CRDs,
all of which are represented as *unstructured.Unstructured.

/lgtm
/approve


TIC_80-Coding-Train-Logo

A version of the Coding Train logo in the Tic 80 fantasy computer.

Variation

Tic-80 (lua) hard-coded Coding Train Logo
Alesk 69
The logo can be seen on the Tic-80 official website: https:/tic80.com/play?cart=3581
More information about the Tic-80 fantasy computer: https://tic80.com/learn

Thank you very much!
I've modified a bit the description in the README.
I've tried to add a screen shot but I haven't managed to do it. How can I add one? I'm sorry for the trouble I'm not very confident with Github and I'm afraid to mess things up!


I24 tests still broken

In test_device_creation() in test_i24, setup is incorrect such that not all i24 devices are created.
Acceptance Criteria

This test always passes
i24 module looks like other beamline modules

For reference, since I rebased the change, here's the version of i24 which was passing with my tests previously.
@patch.object(dodal.utils, "get_beamline_name", return_value="i24")
def test_device_creation(mock, RE):
    mock_live_i24 = reload(i24)
    devices = make_all_devices(mock_live_i24, fake_with_ophyd_sim=True)
    assert len(devices) > 0
    for device_name in devices.keys():
        assert device_name in beamline_utils.ACTIVE_DEVICES
    assert len(beamline_utils.ACTIVE_DEVICES) == len(devices)

    vgonio: VGonio = beamline_utils.ACTIVE_DEVICES["vgonio"]
    assert vgonio.prefix == "BL24I-MO-VGON-01:"
    assert vgonio.kappa.prefix == "BL24I-MO-VGON-01:KAPPA"
    beamline_utils.clear_devices()
    del mock_live_i24


Add 5px bottom margin to bullet-less list items

On small screens list items have no bottom margin (with a 5px bottom margin being applied at tablet and above)
When the govuk-list class is applied on it's own without any modifier, the list items appear to run into each other on mobile, as the spacing between the list items is the same as the spacing between each line.
(When a bullet or number modifier is added e.g. class="govuk-list govuk-list--bullet" the bullet or number indicates the start of a new list item, so the spacing does not need to be adjusted in that case.)
This change applies the spacing to the govuk-list class for all breakpoints, then adjusts the behaviour when bullet or number modifiers are added.
Co-authored-by: David House<EMAIL_ADDRESS>

This is basically Dave's suggested implementation from https://github.com/alphagov/govuk-frontend/issues/1069, so I've added him as a co-author – but we didn't actually pair on this work.


New search UI button keeps active state while pressing ESC

Check for existing issues

[X] Completed

Describe the bug / provide steps to reproduce it

Klick search button (search button should be purple)
Press ESC (search button should still be purple)

If you are using a shortcut (CMD + f) to show search UI and the press ESC, the state of the search button will reset correctly
Environment
Zed: v0.101.0 (preview)
OS: macOS 14.0.0
Memory: 16 GiB
Architecture: aarch64
If applicable, add mockups / screenshots to help explain present your vision of the feature
https://github.com/zed-industries/community/assets/62463826/a54771b8-4b4e-4ba9-bc01-dca87b0a2f8d
If applicable, attach your ~/Library/Logs/Zed/Zed.log file to this issue.
If you only need the most recent lines, you can run the zed: open log command palette action to see the last 1000.
No response

Hey @RemcoSmitsDev, I'm only able to reproduce this if I ensure that I'm focused on the editor, before hitting esc. so for me, the steps are:

Open the buffer seach
Focus back on the editor
HIt escape, notice button is in wrong state.

2 observations:

It didnt matter for me if I used cmd-f or the button to open the buffer search, I was able to reproduce the issue in both cases
When the button is in its incorrect state, focusing on another part of the editor, or focusing outside of the editor causes the button to snap back into its correct state.

cc @osiewicz


Expose polling mechanism for buttons

Is there a way to expose a polling mechanism as opposed to the blocking process you have right now? Related to this post:
https://stackoverflow.com/questions/62376239/rust-tokio-infinite-loop-for-multiple-buttons-listening

hey there,
rust_gpiozero uses rppal under the hood. I believe this functionality can be exposed using set_async_interrupt ?
PRs are welcomed :)


Buttons Click Tracking

I have a problem with the tracking button, there are more clicks on the tracking button than people reading the message, why is this?

Enfrentando o mesmo problema aqui

Due to a recent change with the Teams client, the strategy we used to track reads is being affected. We are working in a fix that will be release in a few days.

For everybody using master-v5.30, you just need to resync the App Service and all functions. For the ones using master-v5.31 it is required to create a new front door rule according to the following screenshot

It was fixed for the versions master-v4.51, master-v5.30 and master-v5.31


question: can we use verso by simply adding require verso to the lakefile?

I would like to ask a question about how users can use verso to write documents.
1A. When a user tries to write a document using the verso, do they need to clone the verso code and add their articles to a specific directory ?
2A. Can the verso syntax and commands for outputting HTML be made available simply by adding a dependency on verso to the lakefile?
2A would be more user-friendly; if not 2A, is it possible to make it like 2A?
I apologise if I have been careless and have missed the written explanation.

No, there's no explanation yet to miss :-)
One difference between Verso and most documentation tools is that Verso isn't really a tool per se - it's a library for building a documentation tool that closely integrates with Lean. This is because different kinds of documents have different needs, and no single tool will serve them all well - mdbook would be a poor fit for blogging, for instance.
The way you'll use Verso, once it makes a bit more progress, is to pick one of the tools implemented with it and then follow that tool's instructions. For now, there's an examples directory that you can refer to, but things are still in flux and not quite ready for general use.


react students login from

We are going to provide a UI for the contractors to have clear view of what there are up to.

thank you for showing your interest on the project and the community as well.

Here are png and files of the form

here its figma file as well
https://www.figma.com/file/Lwg33LOi5rING3BRiVm8bP/Untitled?node-id=1%3A14

i would love to work on this task,kindly assign to me

Ok Go ahead


support journal files

Problem
systemd .journal files are common and will become more common.  Not being able to process a .journal file loses very important information (which degrades the utility of this project).
Solution
Support processing .journal files.  They are remarkably different than processing ad-hoc syslog files, so the strategies within super-speedy-syslog-search will not apply.  However, they are designed well and should be fast to process.
A "journal processor class" would be adjacent to a SyslogProcessor. In other words, all functionality of a SyslogProcessor (and it's contained SyslineReader, LineReader, BlockReader) would be created anew in some JournalProcessor "class".
Here is a technical description of .journal file format (archived).

Implemented JournalReader with capability of re-ordering entries based on either _SOURCE_REALTIME_TIMESTAMP or __REALTIME_TIMESTAMP.
But I found using _SOURCE_REALTIME_TIMESTAMP for order or printing is more misleading than always using __REALTIME_TIMESTAMP.
I added a permanent override pub const DT_USES_SOURCE_OVERRIDE to force always using __REALTIME_TIMESTAMP.
journalctl prints in order of journal entries enumerated but will prefer to print the datetime found in field optional _SOURCE_REALTIME_TIMESTAMP before the mandatory field __REALTIME_TIMESTAMP. This can be very confusing as _SOURCE_REALTIME_TIMESTAMP has more "jitter", __REALTIME_TIMESTAMP is reliably chronological.
Similar observation made in https://github.com/systemd/systemd/issues/10020


[service] Non-provisioned VM blocks Image deletion; Image doesn't take a lease on the backing blob

I found what look like at least two different service issues today.
Basically, I've got an Image that I can't delete, and whose backing blob no longer exists. Neither of these seem like situations I should be able to get into.
Note: I think some of this is specifically because the VM I booted didn't report successful provisioning to the platform, so Azure thinks the VM is still booting. It's unclear though, why this would block the Image deletion. Presumably at this time, the Image was copied to a new blob for the OS Disk... but maybe there are backend COW optimizations...?
Repro

Create an RG "aznixos"
Create a Storage account and container in that RG
Upload a VHD to the storage container
Make an "Image" from the VHD Blob.
Create a new RG "colemick-nixos-20180423"
Create a VM using the Image from the other resource group
Later, decide you don't want that image anymore.
Delete the aznixos resource group

Expected: The resource group is deleted.
Alternative Expectation: The resource group is NOT deleted, because the Image took a lease on the backing blob, which would then prevent the
Actual: The RG fails to delete after sometime (an hour?). Manually attempting to delete the Image results in this error: (which is amusing, at this point in time, the backing blob for the Image doesn't exist, so the Image is probably useless anyway)
Operation Not Allowed
Operation 'Image Delete' is not allowed since the Virtual Machines 'colemick-nixosdev' are being provisioned using the Image 'nixos-image-16.09.1694.019dcc3-x86_64-linux-vhd'.

Issues
From my deduction, it seems like there might be three issues:

Why didn't the Image take a lease out on the blob?
Why does the VM block image deletion? It appears that a user can block Image deletion by booting a VM that doesn't complete provisionig.
Why does ARM just keep retrying this delete?

While looking into this, I've noticed other oddities:

I'd noticed this literally all the time when using Azure, but hte Activity Log is completely unreliable. There was no evidence of my attempt to delete the aznixos group in the Activity Log, despite having done in multiple times. I would've assumed the Activity Log accuracy would be important, but it just doesn't seem that way.

The resource group just reverted back to "Success!" after the deletion failed. That just doesn't seem quite right.

cc: @yugangw-msft

I will try to repro at my end. 2 things maybe you can clarify here(hope you can still remember the thing happened at 9 days ago)

Regarding Make an "Image" from the VHD Blob., I assume you use az image create to create it, right?
Regarding Create a VM using the Image, did the VM successfully get created? I mean if you use az vm show, did the provision state showed as "Success"?

My guess is the vm was still holding to the image for reasons to be figure out here. If you delete the vm first, then  deleting aznixos might go through.

Yes, that is correct. And the only way I know to do that for now, is to create a storage account/container first, then put the VHD there. (I had for a while, but have since removed the "create an MD" step in between the upload and th az image create. It doesn't seem necessary and I need a storage account anyway since I'm uploading the actual raw VHD file myself.)

Yes, the VM was created and I was happily using it for a few days. However, the images I'm creating have a ~buggy agent. They don't always report provisioning. When I was in the Portal, I noticed that the VM was marked specially to indicate this. Further, the error message hints at the image being locked due to a VM still being in provisionig.

(I'm wondering outloud, maybe the underlying blob is locked due to COW optimizations for VMs booted from the images...)

please reactivate once you get more information

It was a custom built image that didn't need provisioning and didn't
include the agent. I think that was the cause, since the platform thought
it never finished provisioning. Anyway, I'm no longer using Azure so we can
leave this closed.
On Wed, Aug 8, 2018, 10:33 AM Yugang Wang<EMAIL_ADDRESS>wrote:

Closed #6254 https://github.com/Azure/azure-cli/issues/6254.
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update ecMouseGEM based on v1.1.0

MATLAB is selecting SOFTWARE OPENGL rendering.
                                                                          < M A T L A B (R) >
                                                                Copyright 1984-2020 The MathWorks, Inc.
                                                            R2020b Update 3 (<IP_ADDRESS>8559) 64-bit (glnxa64)
                                                                           November 23, 2020

To get started, type doc.
For product information, visit www.mathworks.com.

GECKO: Adding enzyme constraints to a genome-scale model

Getting genome-scale model ready...[Warning: Potentially problematic ") AND (", ") AND" or "AND ("relationships found in

grRule #MA_07161: (Polr3g or Polr3gl) and (Papola or Papolb or Papolg or Tent2) and (Tut1 or Tut4 or Tut7) and Gm14567 and Mtpap and Polr1a and Polr1b and Polr1c and Polr1d
and Polr1e and Polr2a and Polr2b and Polr2c and Polr2d and Polr2e and Polr2f and Polr2g and Polr2h and Polr2i and Polr2j and Polr2l and Polr3a and Polr3b and Polr3c and Polr3d
and Polr3e and Polr3f and Polr3h and Polr3k and Polrmt
grRule #MA_07162: (Polr3g or Polr3gl) and (Papola or Papolb or Papolg or Tent2) and (Tut1 or Tut4 or Tut7) and Gm14567 and Mtpap and Polr1a and Polr1b and Polr1c and Polr1d
and Polr1e and Polr2a and Polr2b and Polr2c and Polr2d and Polr2e and Polr2f and Polr2g and Polr2h and Polr2i and Polr2j and Polr2l and Polr3a and Polr3b and Polr3c and Polr3d
and Polr3e and Polr3f and Polr3h and Polr3k and Polrmt
grRule #MA_02512: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_02513: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_02410: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_02411: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03464: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03468: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03469: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_01166: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_01168: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_01209: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_01211: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_01258: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_01260: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_01275: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_01277: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_01293: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_01294: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_01300: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_01301: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03059: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03060: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03064: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03065: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03068: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03069: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03072: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03073: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03076: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03077: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03080: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03081: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03084: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03085: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03088: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03089: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03092: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03093: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03096: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03097: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03100: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03101: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03104: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03328: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03329: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03332: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03333: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03336: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03337: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03340: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03341: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03344: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03345: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03348: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03349: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03352: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03353: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03367: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03368: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03372: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03373: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03503: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03505: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03509: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03510: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03514: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03515: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03304: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03305: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03309: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03310: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03314: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03315: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03319: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03320: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03358: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03359: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03362: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03363: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_01644: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_01642: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_01646: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_01706: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_01708: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #ATPasel: ((Atp6v0a4 and Atp6v0b and Atp6v0c and Atp6v0d2 and Atp6v0e) or (Atp6v0a2 and Atp6v0b and Atp6v0c and Atp6v0d2 and Atp6v0e) or (Atp6v0a4 and Atp6v0b and
Atp6v0c and Atp6v0d1 and Atp6v0e) or (Atp6v0a1 and Atp6v0b and Atp6v0c and Atp6v0d2 and Atp6v0e) or (Atp6v0a1 and Atp6v0b and Atp6v0c and Atp6v0d1 and Atp6v0e) or (Atp6v0b and
Atp6v0c and Atp6v0d1 and Atp6v0e and Tcirg1) or (Atp6v0a2 and Atp6v0b and Atp6v0c and Atp6v0d1 and Atp6v0e) or (Atp6v0b and Atp6v0c and Atp6v0d2 and Atp6v0e and Tcirg1)) and
((Atp6v1a and Atp6v1b2 and Atp6v1c2 and Atp6v1d and Atp6v1e2 and Atp6v1f and Atp6v1g2 and Atp6v1h) or (Atp6v1a and Atp6v1b2 and Atp6v1c1 and Atp6v1d and Atp6v1e1 and Atp6v1f and
Atp6v1g2 and Atp6v1h) or (Atp6v1a and Atp6v1b1 and Atp6v1c1 and Atp6v1d and Atp6v1e1 and Atp6v1f and Atp6v1g3 and Atp6v1h) or (Atp6v1a and Atp6v1b2 and Atp6v1c2 and Atp6v1d and
Atp6v1e2 and Atp6v1f and Atp6v1g3 and Atp6v1h) or (Atp6v1a and Atp6v1b1 and Atp6v1c2 and Atp6v1d and Atp6v1e1 and Atp6v1f and Atp6v1g2 and Atp6v1h) or (Atp6v1a and Atp6v1b1 and
Atp6v1c2 and Atp6v1d and Atp6v1e2 and Atp6v1f and Atp6v1g2 and Atp6v1h) or (Atp6v1a and Atp6v1b1 and Atp6v1c1 and Atp6v1d and Atp6v1e1 and Atp6v1f and Atp6v1g2 and Atp6v1h) or
(Atp6v1a and Atp6v1b2 and Atp6v1c1 and Atp6v1d and Atp6v1e2 and Atp6v1f and Atp6v1g3 and Atp6v1h) or (Atp6v1a and Atp6v1b2 and Atp6v1c1 and Atp6v1d and Atp6v1e1 and Atp6v1f and
Atp6v1g3 and Atp6v1h) or (Atp6v1a and Atp6v1b1 and Atp6v1c1 and Atp6v1d and Atp6v1e2 and Atp6v1f and Atp6v1g2 and Atp6v1h) or (Atp6v1a and Atp6v1b1 and Atp6v1c1 and Atp6v1d and
Atp6v1e2 and Atp6v1f and Atp6v1g3 and Atp6v1h) or (Atp6v1a and Atp6v1b2 and Atp6v1c2 and Atp6v1d and Atp6v1e1 and Atp6v1f and Atp6v1g3 and Atp6v1h) or (Atp6v1a and Atp6v1b2 and
Atp6v1c2 and Atp6v1d and Atp6v1e1 and Atp6v1f and Atp6v1g2 and Atp6v1h) or (Atp6v1a and Atp6v1b1 and Atp6v1c2 and Atp6v1d and Atp6v1e1 and Atp6v1f and Atp6v1g3 and Atp6v1h) or
(Atp6v1a and Atp6v1b1 and Atp6v1c2 and Atp6v1d and Atp6v1e2 and Atp6v1f and Atp6v1g3 and Atp6v1h) or (Atp6v1a and Atp6v1b1 and Atp6v1c2 and Atp6v1d and Atp6v1e2 and Atp6v1f and
Atp6v1g1 and Atp6v1h) or (Atp6v1a and Atp6v1b1 and Atp6v1c2 and Atp6v1d and Atp6v1e1 and Atp6v1f and Atp6v1g1 and Atp6v1h) or (Atp6v1a and Atp6v1b2 and Atp6v1c2 and Atp6v1d and]
[  Atp6v1e1 and Atp6v1f and Atp6v1g1 and Atp6v1h) or (Atp6v1a and Atp6v1b2 and Atp6v1c1 and Atp6v1d and Atp6v1e2 and Atp6v1f and Atp6v1g1 and Atp6v1h) or (Atp6v1a and Atp6v1b1 and
Atp6v1c1 and Atp6v1d and Atp6v1e2 and Atp6v1f and Atp6v1g1 and Atp6v1h) or (Atp6v1a and Atp6v1b2 and Atp6v1c2 and Atp6v1d and Atp6v1e2 and Atp6v1f and Atp6v1g1 and Atp6v1h) or
(Atp6v1a and Atp6v1b2 and Atp6v1c1 and Atp6v1d and Atp6v1e1 and Atp6v1f and Atp6v1g1 and Atp6v1h) or (Atp6v1a and Atp6v1b1 and Atp6v1c1 and Atp6v1d and Atp6v1e1 and Atp6v1f and
Atp6v1g1 and Atp6v1h) or (Atp6v1a and Atp6v1b2 and Atp6v1c1 and Atp6v1d and Atp6v1e2 and Atp6v1f and Atp6v1g2 and Atp6v1h))
grRule #FAOXC16080x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC180x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC183806x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC18480x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC200180x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC2051843x: ((Acaa1a or Acaa1b) and Acox1 and Ehhadh) or ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4)
grRule #FAOXC2242046x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC2252053x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC226205x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC240200x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC241181x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC2442246x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC2452253x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC2452256x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC246226x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC260240x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #PEROXx: (Acaa1a or Acaa1b) and Acox3 and Ehhadh and Hsd17b4
grRule #r1481: (Acaa2 and Hadhb) or ((Acaa1a or Acaa1b) and Hadhb)
grRule #FAOXC101C8x: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #FAOXC102C81x: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #FAOXC10C8x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC10DCC8DCx: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC11BRC9BRx: (Acaa1a or Acaa1b) and Acox3 and Ehhadh and Hsd17b4
grRule #FAOXC121C10x: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #FAOXC123C102x: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #FAOXC12C10x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC12DCC10DCx: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC13BRC11BRx: (Acaa1a or Acaa1b) and Acox3 and Ehhadh and Hsd17b4
grRule #FAOXC141C121x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC142C122x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC143C123x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC14C12x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC14DCC12DCx: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC15BRC13BRx: (Acaa1a or Acaa1b) and Acox3 and Ehhadh and Hsd17b4
grRule #FAOXC161C141x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC163C142x: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #FAOXC164C143x: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #FAOXC16C14x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC16DCC14DCx: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC181C161x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC184C163x: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #FAOXC184C164x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC201C181x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC205C184x: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #FAOXC221C201x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC225C204x: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #FAOXC22C20x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC241C221x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC24C22x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC61C4x: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #FAOXC6C4x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC6DCC4DCx: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC81C61x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC8C6x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC8DCC6DCx: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FOAXC122C101x: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4

This kind of relationships should only be present in  reactions catalysed by complexes of isoenzymes e.g.

(G1 or G2) and (G3 or G4)

For these cases modify the grRules manually, writing all the possible combinations e.g.

(G1 and G3) or (G1 and G4) or (G2 and G3) or (G2 and G4)

For other cases modify the correspondent grRules avoiding:

Overall container brackets, e.g.
"(G1 and G2)" should be "G1 and G2"

Single unit enzymes enclosed into brackets, e.g.
"(G1)" should be "G1"

The use of uppercases for logical operators, e.g.
"G1 OR G2" should be "G1 or G2"

Unbalanced brackets, e.g.
"((G1 and G2) or G3" should be "(G1 and G2) or G3"
]
[> In standardizeGrRules>findPotentialErrors (line 155)
In standardizeGrRules (line 38)
In preprocessModel (line 27)
In enhanceGEM (line 51)]
Done!

==================
Generating ecModel:
Retrieving EC numbers...WARNING: Potentially problematic ") AND (" in the grRules for reaction(s):
MA_07161
MA_07162
MA_02512
MA_02513
MA_02410
MA_02411
MA_03464
MA_03468
MA_03469
...and 133 more
................................................................................................................................... Done!
Matching kcats...................................................................................................................................... Done!
Adding enzymes to reactions.................................................................................................................................................................................................... Done!
Improving model with curated data...[Warning: Potentially problematic ") AND (", ") AND" or "AND ("relationships found in

grRule #MA_07161: (Polr3g or Polr3gl) and (Papola or Papolb or Papolg or Tent2) and (Tut1 or Tut4 or Tut7) and Gm14567 and Mtpap and Polr1a and Polr1b and Polr1c and Polr1d
and Polr1e and Polr2a and Polr2b and Polr2c and Polr2d and Polr2e and Polr2f and Polr2g and Polr2h and Polr2i and Polr2j and Polr2l and Polr3a and Polr3b and Polr3c and Polr3d
and Polr3e and Polr3f and Polr3h and Polr3k and Polrmt
grRule #MA_07162: (Polr3g or Polr3gl) and (Papola or Papolb or Papolg or Tent2) and (Tut1 or Tut4 or Tut7) and Gm14567 and Mtpap and Polr1a and Polr1b and Polr1c and Polr1d
and Polr1e and Polr2a and Polr2b and Polr2c and Polr2d and Polr2e and Polr2f and Polr2g and Polr2h and Polr2i and Polr2j and Polr2l and Polr3a and Polr3b and Polr3c and Polr3d
and Polr3e and Polr3f and Polr3h and Polr3k and Polrmt
grRule #MA_02512: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_02513: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_02410: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_02411: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03464: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03468: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03469: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_01166: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_01168: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_01209: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_01211: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_01258: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_01260: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_01275: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_01277: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_01293: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_01294: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_01300: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_01301: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03059: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03060: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03064: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03065: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03068: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03069: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03072: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03073: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03076: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03077: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03080: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03081: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03084: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03085: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03088: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03089: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03092: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03093: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03096: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03097: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03100: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03101: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03104: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03328: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03329: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03332: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03333: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03336: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03337: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03340: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03341: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03344: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03345: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03348: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03349: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03352: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03353: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03367: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03368: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03372: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03373: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03503: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03505: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03509: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03510: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03514: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03515: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03304: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03305: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03309: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03310: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03314: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03315: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03319: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03320: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03358: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03359: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03362: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03363: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_01644: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_01642: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_01646: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_01706: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_01708: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #ATPasel: ((Atp6v0a4 and Atp6v0b and Atp6v0c and Atp6v0d2 and Atp6v0e) or (Atp6v0a2 and Atp6v0b and Atp6v0c and Atp6v0d2 and Atp6v0e) or (Atp6v0a4 and Atp6v0b and
Atp6v0c and Atp6v0d1 and Atp6v0e) or (Atp6v0a1 and Atp6v0b and Atp6v0c and Atp6v0d2 and Atp6v0e) or (Atp6v0a1 and Atp6v0b and Atp6v0c and Atp6v0d1 and Atp6v0e) or (Atp6v0b and
Atp6v0c and Atp6v0d1 and Atp6v0e and Tcirg1) or (Atp6v0a2 and Atp6v0b and Atp6v0c and Atp6v0d1 and Atp6v0e) or (Atp6v0b and Atp6v0c and Atp6v0d2 and Atp6v0e and Tcirg1)) and
((Atp6v1a and Atp6v1b2 and Atp6v1c2 and Atp6v1d and Atp6v1e2 and Atp6v1f and Atp6v1g2 and Atp6v1h) or (Atp6v1a and Atp6v1b2 and Atp6v1c1 and Atp6v1d and Atp6v1e1 and Atp6v1f and
Atp6v1g2 and Atp6v1h) or (Atp6v1a and Atp6v1b1 and Atp6v1c1 and Atp6v1d and Atp6v1e1 and Atp6v1f and Atp6v1g3 and Atp6v1h) or (Atp6v1a and Atp6v1b2 and Atp6v1c2 and Atp6v1d and
Atp6v1e2 and Atp6v1f and Atp6v1g3 and Atp6v1h) or (Atp6v1a and Atp6v1b1 and Atp6v1c2 and Atp6v1d and Atp6v1e1 and Atp6v1f and Atp6v1g2 and Atp6v1h) or (Atp6v1a and Atp6v1b1 and
Atp6v1c2 and Atp6v1d and Atp6v1e2 and Atp6v1f and Atp6v1g2 and Atp6v1h) or (Atp6v1a and Atp6v1b1 and Atp6v1c1 and Atp6v1d and Atp6v1e1 and Atp6v1f and Atp6v1g2 and Atp6v1h) or
(Atp6v1a and Atp6v1b2 and Atp6v1c1 and Atp6v1d and Atp6v1e2 and Atp6v1f and Atp6v1g3 and Atp6v1h) or (Atp6v1a and Atp6v1b2 and Atp6v1c1 and Atp6v1d and Atp6v1e1 and Atp6v1f and
Atp6v1g3 and Atp6v1h) or (Atp6v1a and Atp6v1b1 and Atp6v1c1 and Atp6v1d and Atp6v1e2 and Atp6v1f and Atp6v1g2 and Atp6v1h) or (Atp6v1a and Atp6v1b1 and Atp6v1c1 and Atp6v1d and
Atp6v1e2 and Atp6v1f and Atp6v1g3 and Atp6v1h) or (Atp6v1a and Atp6v1b2 and Atp6v1c2 and Atp6v1d and Atp6v1e1 and Atp6v1f and Atp6v1g3 and Atp6v1h) or (Atp6v1a and Atp6v1b2 and
Atp6v1c2 and Atp6v1d and Atp6v1e1 and Atp6v1f and Atp6v1g2 and Atp6v1h) or (Atp6v1a and Atp6v1b1 and Atp6v1c2 and Atp6v1d and Atp6v1e1 and Atp6v1f and Atp6v1g3 and Atp6v1h) or
(Atp6v1a and Atp6v1b1 and Atp6v1c2 and Atp6v1d and Atp6v1e2 and Atp6v1f and Atp6v1g3 and Atp6v1h) or (Atp6v1a and Atp6v1b1 and Atp6v1c2 and Atp6v1d and Atp6v1e2 and Atp6v1f and
Atp6v1g1 and Atp6v1h) or (Atp6v1a and Atp6v1b1 and Atp6v1c2 and Atp6v1d and Atp6v1e1 and Atp6v1f and Atp6v1g1 and Atp6v1h) or (Atp6v1a and Atp6v1b2 and Atp6v1c2 and Atp6v1d and]
[  Atp6v1e1 and Atp6v1f and Atp6v1g1 and Atp6v1h) or (Atp6v1a and Atp6v1b2 and Atp6v1c1 and Atp6v1d and Atp6v1e2 and Atp6v1f and Atp6v1g1 and Atp6v1h) or (Atp6v1a and Atp6v1b1 and
Atp6v1c1 and Atp6v1d and Atp6v1e2 and Atp6v1f and Atp6v1g1 and Atp6v1h) or (Atp6v1a and Atp6v1b2 and Atp6v1c2 and Atp6v1d and Atp6v1e2 and Atp6v1f and Atp6v1g1 and Atp6v1h) or
(Atp6v1a and Atp6v1b2 and Atp6v1c1 and Atp6v1d and Atp6v1e1 and Atp6v1f and Atp6v1g1 and Atp6v1h) or (Atp6v1a and Atp6v1b1 and Atp6v1c1 and Atp6v1d and Atp6v1e1 and Atp6v1f and
Atp6v1g1 and Atp6v1h) or (Atp6v1a and Atp6v1b2 and Atp6v1c1 and Atp6v1d and Atp6v1e2 and Atp6v1f and Atp6v1g2 and Atp6v1h))
grRule #FAOXC16080x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC180x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC183806x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC18480x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC200180x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC2051843x: ((Acaa1a or Acaa1b) and Acox1 and Ehhadh) or ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4)
grRule #FAOXC2242046x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC2252053x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC226205x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC240200x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC241181x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC2442246x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC2452253x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC2452256x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC246226x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC260240x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #PEROXx: (Acaa1a or Acaa1b) and Acox3 and Ehhadh and Hsd17b4
grRule #r1481: (Acaa2 and Hadhb) or ((Acaa1a or Acaa1b) and Hadhb)
grRule #FAOXC101C8x: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #FAOXC102C81x: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #FAOXC10C8x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC10DCC8DCx: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC11BRC9BRx: (Acaa1a or Acaa1b) and Acox3 and Ehhadh and Hsd17b4
grRule #FAOXC121C10x: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #FAOXC123C102x: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #FAOXC12C10x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC12DCC10DCx: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC13BRC11BRx: (Acaa1a or Acaa1b) and Acox3 and Ehhadh and Hsd17b4
grRule #FAOXC141C121x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC142C122x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC143C123x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC14C12x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC14DCC12DCx: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC15BRC13BRx: (Acaa1a or Acaa1b) and Acox3 and Ehhadh and Hsd17b4
grRule #FAOXC161C141x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC163C142x: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #FAOXC164C143x: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #FAOXC16C14x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC16DCC14DCx: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC181C161x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC184C163x: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #FAOXC184C164x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC201C181x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC205C184x: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #FAOXC221C201x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC225C204x: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #FAOXC22C20x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC241C221x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC24C22x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC61C4x: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #FAOXC6C4x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC6DCC4DCx: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC81C61x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC8C6x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC8DCC6DCx: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FOAXC122C101x: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03468_REV: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03469_REV: (Acaa1a or Acaa1b) and Myo5b

This kind of relationships should only be present in  reactions catalysed by complexes of isoenzymes e.g.

(G1 or G2) and (G3 or G4)

For these cases modify the grRules manually, writing all the possible combinations e.g.

(G1 and G3) or (G1 and G4) or (G2 and G3) or (G2 and G4)

For other cases modify the correspondent grRules avoiding:

Overall container brackets, e.g.
"(G1 and G2)" should be "G1 and G2"

Single unit enzymes enclosed into brackets, e.g.
"(G1)" should be "G1"

The use of uppercases for logical operators, e.g.
"G1 OR G2" should be "G1 or G2"

Unbalanced brackets, e.g.
"((G1 and G2) or G3" should be "(G1 and G2) or G3"
]
[> In standardizeGrRules>findPotentialErrors (line 155)
In standardizeGrRules (line 38)
In manualModifications (line 4)
In enhanceGEM (line 65)]
Done!
Removing repeated rxn: MA_06621 & RE0456M_REV
Removing repeated rxn: C181CPT1 & C181CPT2rbc_REV
Removing repeated rxn: r2346 & WHARACHDtd_REV
Removing repeated rxn: RE0456M & MA_06621_REV
Removing repeated rxn: WHARACHDtd & r2346_REV
Removing repeated rxn: C181CPT2rbc & C181CPT1_REV
[Warning: Potentially problematic ") AND (", ") AND" or "AND ("relationships found in

grRule #MA_07161: (Polr3g or Polr3gl) and (Papola or Papolb or Papolg or Tent2) and (Tut1 or Tut4 or Tut7) and Gm14567 and Mtpap and Polr1a and Polr1b and Polr1c and Polr1d
and Polr1e and Polr2a and Polr2b and Polr2c and Polr2d and Polr2e and Polr2f and Polr2g and Polr2h and Polr2i and Polr2j and Polr2l and Polr3a and Polr3b and Polr3c and Polr3d
and Polr3e and Polr3f and Polr3h and Polr3k and Polrmt
grRule #MA_07162: (Polr3g or Polr3gl) and (Papola or Papolb or Papolg or Tent2) and (Tut1 or Tut4 or Tut7) and Gm14567 and Mtpap and Polr1a and Polr1b and Polr1c and Polr1d
and Polr1e and Polr2a and Polr2b and Polr2c and Polr2d and Polr2e and Polr2f and Polr2g and Polr2h and Polr2i and Polr2j and Polr2l and Polr3a and Polr3b and Polr3c and Polr3d
and Polr3e and Polr3f and Polr3h and Polr3k and Polrmt
grRule #MA_02512: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_02513: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_02410: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_02411: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03464: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03468: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03469: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_01166: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_01168: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_01209: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_01211: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_01258: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_01260: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_01275: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_01277: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_01293: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_01294: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_01300: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_01301: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03059: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03060: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03064: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03065: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03068: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03069: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03072: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03073: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03076: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03077: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03080: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03081: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03084: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03085: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03088: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03089: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03092: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03093: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03096: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03097: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03100: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03101: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03104: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03328: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03329: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03332: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03333: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03336: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03337: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03340: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03341: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03344: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03345: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03348: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03349: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03352: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03353: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03367: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03368: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03372: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03373: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03503: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03505: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03509: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03510: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03514: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03515: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03304: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03305: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03309: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03310: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03314: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03315: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03319: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03320: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03358: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03359: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_03362: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03363: (Acaa1a or Acaa1b) and Myo5b
grRule #MA_01644: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_01642: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_01646: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_01706: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_01708: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #ATPasel: ((Atp6v0a4 and Atp6v0b and Atp6v0c and Atp6v0d2 and Atp6v0e) or (Atp6v0a2 and Atp6v0b and Atp6v0c and Atp6v0d2 and Atp6v0e) or (Atp6v0a4 and Atp6v0b and
Atp6v0c and Atp6v0d1 and Atp6v0e) or (Atp6v0a1 and Atp6v0b and Atp6v0c and Atp6v0d2 and Atp6v0e) or (Atp6v0a1 and Atp6v0b and Atp6v0c and Atp6v0d1 and Atp6v0e) or (Atp6v0b and
Atp6v0c and Atp6v0d1 and Atp6v0e and Tcirg1) or (Atp6v0a2 and Atp6v0b and Atp6v0c and Atp6v0d1 and Atp6v0e) or (Atp6v0b and Atp6v0c and Atp6v0d2 and Atp6v0e and Tcirg1)) and
((Atp6v1a and Atp6v1b2 and Atp6v1c2 and Atp6v1d and Atp6v1e2 and Atp6v1f and Atp6v1g2 and Atp6v1h) or (Atp6v1a and Atp6v1b2 and Atp6v1c1 and Atp6v1d and Atp6v1e1 and Atp6v1f and
Atp6v1g2 and Atp6v1h) or (Atp6v1a and Atp6v1b1 and Atp6v1c1 and Atp6v1d and Atp6v1e1 and Atp6v1f and Atp6v1g3 and Atp6v1h) or (Atp6v1a and Atp6v1b2 and Atp6v1c2 and Atp6v1d and
Atp6v1e2 and Atp6v1f and Atp6v1g3 and Atp6v1h) or (Atp6v1a and Atp6v1b1 and Atp6v1c2 and Atp6v1d and Atp6v1e1 and Atp6v1f and Atp6v1g2 and Atp6v1h) or (Atp6v1a and Atp6v1b1 and
Atp6v1c2 and Atp6v1d and Atp6v1e2 and Atp6v1f and Atp6v1g2 and Atp6v1h) or (Atp6v1a and Atp6v1b1 and Atp6v1c1 and Atp6v1d and Atp6v1e1 and Atp6v1f and Atp6v1g2 and Atp6v1h) or
(Atp6v1a and Atp6v1b2 and Atp6v1c1 and Atp6v1d and Atp6v1e2 and Atp6v1f and Atp6v1g3 and Atp6v1h) or (Atp6v1a and Atp6v1b2 and Atp6v1c1 and Atp6v1d and Atp6v1e1 and Atp6v1f and
Atp6v1g3 and Atp6v1h) or (Atp6v1a and Atp6v1b1 and Atp6v1c1 and Atp6v1d and Atp6v1e2 and Atp6v1f and Atp6v1g2 and Atp6v1h) or (Atp6v1a and Atp6v1b1 and Atp6v1c1 and Atp6v1d and
Atp6v1e2 and Atp6v1f and Atp6v1g3 and Atp6v1h) or (Atp6v1a and Atp6v1b2 and Atp6v1c2 and Atp6v1d and Atp6v1e1 and Atp6v1f and Atp6v1g3 and Atp6v1h) or (Atp6v1a and Atp6v1b2 and
Atp6v1c2 and Atp6v1d and Atp6v1e1 and Atp6v1f and Atp6v1g2 and Atp6v1h) or (Atp6v1a and Atp6v1b1 and Atp6v1c2 and Atp6v1d and Atp6v1e1 and Atp6v1f and Atp6v1g3 and Atp6v1h) or
(Atp6v1a and Atp6v1b1 and Atp6v1c2 and Atp6v1d and Atp6v1e2 and Atp6v1f and Atp6v1g3 and Atp6v1h) or (Atp6v1a and Atp6v1b1 and Atp6v1c2 and Atp6v1d and Atp6v1e2 and Atp6v1f and
Atp6v1g1 and Atp6v1h) or (Atp6v1a and Atp6v1b1 and Atp6v1c2 and Atp6v1d and Atp6v1e1 and Atp6v1f and Atp6v1g1 and Atp6v1h) or (Atp6v1a and Atp6v1b2 and Atp6v1c2 and Atp6v1d and]
[  Atp6v1e1 and Atp6v1f and Atp6v1g1 and Atp6v1h) or (Atp6v1a and Atp6v1b2 and Atp6v1c1 and Atp6v1d and Atp6v1e2 and Atp6v1f and Atp6v1g1 and Atp6v1h) or (Atp6v1a and Atp6v1b1 and
Atp6v1c1 and Atp6v1d and Atp6v1e2 and Atp6v1f and Atp6v1g1 and Atp6v1h) or (Atp6v1a and Atp6v1b2 and Atp6v1c2 and Atp6v1d and Atp6v1e2 and Atp6v1f and Atp6v1g1 and Atp6v1h) or
(Atp6v1a and Atp6v1b2 and Atp6v1c1 and Atp6v1d and Atp6v1e1 and Atp6v1f and Atp6v1g1 and Atp6v1h) or (Atp6v1a and Atp6v1b1 and Atp6v1c1 and Atp6v1d and Atp6v1e1 and Atp6v1f and
Atp6v1g1 and Atp6v1h) or (Atp6v1a and Atp6v1b2 and Atp6v1c1 and Atp6v1d and Atp6v1e2 and Atp6v1f and Atp6v1g2 and Atp6v1h))
grRule #FAOXC16080x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC180x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC183806x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC18480x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC200180x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC2051843x: ((Acaa1a or Acaa1b) and Acox1 and Ehhadh) or ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4)
grRule #FAOXC2242046x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC2252053x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC226205x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC240200x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC241181x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC2442246x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC2452253x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC2452256x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC246226x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #FAOXC260240x: ((Acaa1a or Acaa1b) and Acox1 and Hsd17b4) or ((Acaa1a or Acaa1b) and Acox1 and Ehhadh)
grRule #PEROXx: (Acaa1a or Acaa1b) and Acox3 and Ehhadh and Hsd17b4
grRule #r1481: (Acaa2 and Hadhb) or ((Acaa1a or Acaa1b) and Hadhb)
grRule #FAOXC101C8x: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #FAOXC102C81x: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #FAOXC10C8x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC10DCC8DCx: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC11BRC9BRx: (Acaa1a or Acaa1b) and Acox3 and Ehhadh and Hsd17b4
grRule #FAOXC121C10x: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #FAOXC123C102x: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #FAOXC12C10x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC12DCC10DCx: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC13BRC11BRx: (Acaa1a or Acaa1b) and Acox3 and Ehhadh and Hsd17b4
grRule #FAOXC141C121x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC142C122x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC143C123x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC14C12x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC14DCC12DCx: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC15BRC13BRx: (Acaa1a or Acaa1b) and Acox3 and Ehhadh and Hsd17b4
grRule #FAOXC161C141x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC163C142x: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #FAOXC164C143x: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #FAOXC16C14x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC16DCC14DCx: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC181C161x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC184C163x: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #FAOXC184C164x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC201C181x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC205C184x: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #FAOXC221C201x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC225C204x: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #FAOXC22C20x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC241C221x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC24C22x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC61C4x: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #FAOXC6C4x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC6DCC4DCx: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC81C61x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC8C6x: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FAOXC8DCC6DCx: (Acaa1a or Acaa1b) and Acox1 and Ehhadh and Hsd17b4
grRule #FOAXC122C101x: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03468_REV: (Acaa1a or Acaa1b) and Ehhadh and Hsd17b4
grRule #MA_03469_REV: (Acaa1a or Acaa1b) and Myo5b

This kind of relationships should only be present in  reactions catalysed by complexes of isoenzymes e.g.

(G1 or G2) and (G3 or G4)

For these cases modify the grRules manually, writing all the possible combinations e.g.

(G1 and G3) or (G1 and G4) or (G2 and G3) or (G2 and G4)

For other cases modify the correspondent grRules avoiding:

Overall container brackets, e.g.
"(G1 and G2)" should be "G1 and G2"

Single unit enzymes enclosed into brackets, e.g.
"(G1)" should be "G1"

The use of uppercases for logical operators, e.g.
"G1 OR G2" should be "G1 or G2"

Unbalanced brackets, e.g.
"((G1 and G2) or G3" should be "(G1 and G2) or G3"
]
[> In standardizeGrRules>findPotentialErrors (line 155)
In standardizeGrRules (line 38)
In manualModifications (line 61)
In enhanceGEM (line 65)]

==============================================================
Generating ecModel with shared pool assumption (ecModel_batch):
prot_abundance file is empty or not available. A default value of f=0.5 is set instead
Constrained ecModel is feasible
Matching data to enzymes in model...

I'm not sure what's happening here based on the output of the pipeline. Nothing gets added to this PR, but the action terminates after only 15 minutes without a clear error. @IVANDOMENZAIN any thoughts?

@mihai-sysbio, I'm keeping track of the issues here. I've seen that in the latest runs no model files were generated, I realized that we were still using the human protDatabase.mat file, which explains why GECKO never found matches in the databases for the genes in the model. I've uploaded the uniprot part of this file for Mus musculus, but an error popped-up when trying to read an empty array (corresponding to an empty KEGG database in the protDatabase file).  I'm generating the complete protDatabase.mat for mouse locally now, but this step takes some hours (as it should download all the information for this species available in KEGG). Will upload the file as soon as it is ready.

Many thanks @IVANDOMENZAIN. Regarding how the use of the KEGG API slows down the update, could you share your thoughts on https://github.com/SysBioChalmers/GECKO/issues/140 ?

An error message may be added to this pipeline when GECKO couldn't find matches proteins for the genes in a model.

Or if the list is too long, at least the total number of unmatched genes.

I'm closing this issue in favor of #54


Migrate Travis CI to Github Actions

Validated with test release https://github.com/microsoft/ApplicationInsights-node.js-native-metrics/releases/tag/test


stdlib: xml.etree.ElementTree

Hello, I love this project so far and I'm hoping to use it for my own projects but so far the lack of existing standard library modules makes it difficult to integrate with most existing code bases. One of the primary libraries that I use and gets used by many other important libraries are the xml tools.
I would be happy to contribute on helping build out the xml stdlib but it's primarily backed by a cpython parser called pyexpat which is just imported here.
Is there a way to include cpython components to allow for the build of this library or what's the best alternative and approach for implementation?

I suppose I could, but that sort of defeats the purpose of the project, as you mentioned. My hope is to improve the performance of my code base, but if the majority of the libraries I use are still in native python, there isn't much opportunity for improvement.
Appreciate the suggestion nonetheless. Thanks

That sounds less than ideal. Doesn't that just mean importing it directly is an even worse idea? Lol

So it sounds like the best alternative would be to write an xml parser from scratch and include it as part of a new version of the standard library?

I have a very basic tokenizer complete, working on building out a complete parser. My intention is to first build it in standard python and then convert it to use codon's extra features, but I have quite a few questions about implementation.
First, is there a way to implement C-Like (or perhaps even better Rust-Like) Enums in python with Codon?
Second, I noticed that the typing library is completely empty. I couldn't find any docs related to the Optional type. Is there support for the <type> | None syntax?
Last, I noticed in the docs that there weren't many instances where a return type was explicitly declared. It seems pretty obvious that whatever compilation is going on infers the type based on the code and what it returns, but will it be able to handle
processing a type with multiple returns? Is there even a reason or advantage to explicitly stating the return?

Good to know thanks for the reference. Progress is steady on the XML lib. I have to build a lexer/parser for XPATH as well for the search features lol.

Hello, I tried to begin my port to codon after writing most of the base library, but I came across a few issues I'm not sure how to handle.
First: using references before they're defined within the same file.
For example:
def get_a():
   return A()

class A:
    pass

print(get_a())

returns test.codon:2:11-12: error: name 'A' is not defined
This same issue occurs when importing a library at bottom of the file to avoid circular imports.
Example:
# file1.codon:
from file2 import func_c

def func_a():
  func_c()
  print('Hello World!')

# file2.codon:
def func_b():
  func_a()

def func_c():
  print('Function C!')

from file1 import func_a

Second, I'm not sure how Codon handles strings but the lack of a bytes or bytearray type makes it difficult to work with them.
Each have their own specific uses separate from a standard string type and the bytearray especially makes it easy to append to like a list while still acting as a standard bytes object.
At the moment, these two things are keeping me from progressing any further on converting the library since I can't compile anything at the moment. Any help or workaround would be appreciated thanks :)

The scope parsing from top to bottom seems rather restrictive but I understand that implementing more complicated is likely a difficult process. I'll see if it's possible to reorganize the project to avoid import loops then, but it will become a bit tricky when objects depend or re-use one another.
As for the typehints and bytes/bytearray, I look forward to hearing from you. Thanks!

I'm going to close this issue. This project ultimately inspired the creation of my new pyxml library which was originally intended to be ported into a codon implementation of the stdlib xml library, but my motivation has waned due to my frustration with codon's lack of proper compatibility with python3's standard type annotations which seem to be mutually exclusive with the way codon operates.
As a massive lover of typehints, my hope was that codon would be taking the existing typehints in all of my projects and making use of the extra information provided to make compiled optimizations on them but that doesn't seem to be the way codon ultimately behaves or what is intended, which is a shame.
Ultimately, anyone is free to take my pure python implementation and use it as a reference or outright use it to implement it into codon's stdlib, but I'm concluding my efforts until typehints are properly supported if that ever happens. Best of luck to the codon team and contributers!

Hi @imgurbot12 — appreciate the feedback, and sorry to hear that. We are still working on closing the gap with Python and there are definitely a few places that need more attention.
If possible could you please let me know what specific things/incompatibilities gave you trouble? I want to see if/how we can address them.

Looking through the repo you linked… I can see a couple cases we don’t have support for yet but overall this definitely looks like the type of thing that should work in Codon.
Also mentioning @inumanag so he can take a look.

Hi @imgurbot12 — appreciate the feedback, and sorry to hear that. We are still working on closing the gap with Python and there are definitely a few places that need more attention.
If possible could you please let me know what specific things/incompatibilities gave you trouble? I want to see if/how we can address them.

@arshajii, thank you for your response. Happy to include some of the things I noticed and had difficulty with during my implementation efforts. I've ranked everything I would consider most important to least in an ordered list:

bytes / bytearray builtin types do not exist
localized imports don not support dot notation eg: from .local_module import X
Topdown only parsing means you cannot reference types before they are defined
nor can you import a partially initialized module
@classmethod decorator does not exist
Iterator typehint missing
Type typehint missing
Self typehint missing
BinaryIO/TextIO typehints missing
Generator typehint only accepts 1 argument as opposed to python using 3
Enum python stdlib not implemented
Any typehint missing
Protocol/ABC type missing (maybe that's redundant? - might not be nessesary)

Hope that helps. Thanks again :)


Add a LICENSE file

This crate seems to use the MIT license, but does not reproduce the license in the form of a LICENSE file. The MIT license requires reproducing it: https://choosealicense.com/licenses/mit/#

Fixed by #37


Add bundle_rsync_app_path to specify where to run bundle

Capistrano::BundleRsync assumes that the top directory of the repository is the app directory.
Therefore, this runs bundle commands and locates config directory and .bundle/config files there.
This is simple but cannot fully support repositories where app directory locates in the subdirectory from the top directory.
Unlike :git_tree, this feature even support apps which have dependency in other sub directories.
The main use cases of feature is to support multi-apps repository with shared directory.
e.g.
* api-server-1 (depends on shared)
* api-server-2 (depends on shared)
* html-server (depends on shared)
* shared

LGTM. Merge whenever you want

Thank you ❤


_atomic_save with transaction cause "Invalid cross-device link" error

Bug description
I Upgraded my pl verison from 2.0.4 to 2.4. The same training code will have the error below
2024-09-06 23:01:53 [on_validation_epoch_end] collecting matched instance from 64 ranks
2024-09-06 23:02:17 [on_validation_epoch_end] end
Traceback (most recent call last):
  File "/usr/lib/python3.10/shutil.py", line 816, in move
    os.rename(src, real_dst)
OSError: [Errno 18] Invalid cross-device link: '/tmp/tmp7ue72_bg' -> '/xxx/model/ckpt-epoch=000.ckpt'

When I check the corresponding code difference, I find the difference below
@@ -65,8 +78,69 @@ def _atomic_save(checkpoint: Dict[str, Any], filepath: Union[str, Path]) -> None
             accepts.
         filepath: The path to which the checkpoint will be saved.
             This points to the file that the checkpoint will be stored in.
+
     """
     bytesbuffer = io.BytesIO()
+    log.debug(f"Saving checkpoint: {filepath}")
     torch.save(checkpoint, bytesbuffer)
-    with fsspec.open(filepath, "wb") as f:
+
+    # We use a transaction here to avoid file corruption if the save gets interrupted
+    fs, urlpath = fsspec.core.url_to_fs(str(filepath))
+    with fs.transaction, fs.open(urlpath, "wb") as f:
         f.write(bytesbuffer.getvalue())

It seems that the using of transaction will cause the error when moving a file between different filesystem. Is there any solution?
What version are you seeing the problem on?
v2.4
How to reproduce the bug
No response
Error messages and logs
# Error messages and logs here please

Environment

Current environment
#- PyTorch Lightning Version (e.g., 2.4.0):
#- PyTorch Version (e.g., 2.4):
#- Python version (e.g., 3.12):
#- OS (e.g., Linux):
#- CUDA/cuDNN version:
#- GPU models and configuration:
#- How you installed Lightning(`conda`, `pip`, source):

More info
No response

Same thing happening to me on 2.4.0 version, but it works fine on 2.3.1

Same thing happening to me on 2.4.0 version, but it works fine on 2.3.1

Yes, same situation..

Same thing happening for me on version 2.4, but only occasionally, curious why we see this only sometimes?

Same thing happening for me on version 2.5.0.post0.
I wantted to save model checkpoints into disk mounted by Cloud Storage FUSE, but "Invalid cross-device link" error is occured.


Incoherent license

This repo is under the CC-0 license, while the footer contains a CC-BY-NC-SA badge.

I like CC-0 but I don't have much knowledge about licences. What do you think ?

I don't know much either about it, but I feel pretty OK with CC-0: https://choosealicense.com/licenses/cc0-1.0/

Let's go for CC-0 then?

Ok for me.

Licence is now cc-0.


Post with muted word is not hidden if QRTed with an embed

Describe the bug

A post containing a muted word that is then quote reposted with an embed is not hidden.
To Reproduce
Steps to reproduce the behavior:

Create a post with some keyword that is in your muted words list.
Quote repost with any embed (picture, link card, etc)
Post containing mute word is now visible on your timeline.

Expected behavior
A post containing a muted word should be hidden if the post is QRTed with an embed, as it is hidden when QRTed with plain text.
Screenshots

Details

Platform: Desktop web (Edge v122.0.2365.52 on Windows 11 22621.3155) , but also reproducible on iOS 17.3.1
Platform version: 1.70.0 (36)
App version: 1.70.0 (36)

Additional context
I'm not sure if this is a client-side issue or a protocol-side issue, so I'd be happy to move this bug report to the proper place if it's found to not be a social-app issue.
Also, it does seem a bit weird that the rationale text differs between seeing the root post and the post through a quote repost, but I'm not sure if that's intentional or not.

Fixed by https://github.com/bluesky-social/social-app/pull/3071