youngmon/atlassian-qna huggingface dataset:
GPL15088- how to find GAGE
Asked by Eithar Mohamed:

My name is Eithar Mohamed, a PhD student at University of Hull, UK. I want to say thank you for BART developing and open access. I have this dataset GSE34861 and GLP for upregulated and downregulated genes are not available, what can I do?

Secondly, is this system allow to compare 2 or 3 dataset simultaneously.

Best wishes,

Eithar


Answers:
author: Nic Brough -Adaptavist-
body: Welcome to the Atlassian Community!

Could you explain what this has to do with Atlassian software? You have not mentioned any Atlassian stuff in your question, nor explained your acronyms and codes, so we are very stuck here.

I am going to guess that you were reading a documentation site that was hosted in Confluence and you have clicked for "help with documentation system" instead of "help with what it is documenting" (Or maybe your data is being held in Bitbucket, and you've clicked help with BB instead of help with the data)


Tags: server
Receiving an Authentication Failed for bitbucket.org while cloning in GitHub Desktop on a Mac
Asked by Joe Contreras:

Hello,

I'm receiving an Authentication Failed for bitbucket.org while cloning in GitHub Desktop on a Mac.

I created an app password in Bitbucket.

I'm using my Github account to login to the GitHub desktop and want to downloaded a bitbucket repo.

I'm not clear on what the processed is to make this work.

Regards,


Answers:
author: Ben
body: Hi Joe!

Whilst I am not very skilled in providing support for GitHub, I have managed to find documentation from Github which may help. It describes how to import repositories from **Bitbucket Cloud into Github using the Github Importer Tool** :  
<https://docs.github.com/en/get-started/importing-your-projects-to-github/importing-source-code-to-github/importing-a-repository-with-github-importer>

Thanks,

Ben - Bitbucket Cloud Support

comments: author: Rati Dzidziguri
body: I have exact same problem I need to import few repos in Github but the tool stopped working. it authenticates spins for a while and gives me credentials screen again so something is broken for sure.


author: Ben
body: Hey Rati,

This issue might be due to our deprecation of GIT username/password in favour of App Password which took effect progressively from 01/03 onwards to customers:  
<https://community.atlassian.com/t5/Bitbucket-articles/Announcement-Bitbucket-Cloud-account-password-usage-for-Git-over/ba-p/1948231>

Cheers!

- Ben (Bitbucket Cloud)


Tags: bitbucket-cloud

cloud
Pipe.py jenkins trigger from Bitbucket
Asked by Sarath Nagarajan:

Hello Guys,

Could someone help me with this? i started getting this error in pipe.py when i call a jenkins job from bitbucket using pipe in BB.yml  
- step: \&functionalTest  
name: functional test  
image: python:3.9  
script:  
- pipe: atlassian/jenkins-job-trigger:0.1.1  
variables:  
JENKINS_URL: 'myJenkinsURL  
JENKINS_USER: 'myUser'  
JENKINS_TOKEN: $JENKINS_USER_TOKEN  
JOB_NAME: 'job/myJenkinsjob/job/main'  
WAIT: 'true'  
WAIT_MAX_TIMEOUT: 360

Error:  
INFO: Jenkins job job/online-mymorrisons-automation/job/main is PENDING. Wait for build to be started...  
Traceback (most recent call last):  
File "/pipe.py", line 145, in <module>  
pipe.run()  
File "/pipe.py", line 136, in run  
self.wait_for_job(build_response.headers['Location'])  
File "/pipe.py", line 73, in wait_for_job  
build_number = executable.get('number')  
AttributeError: 'NoneType' object has no attribute 'get'  
`Seems the job was triggered in Jenkins; however, BB is not waiting for the Job result back instead it failed the stage whilst the test is still running in Jenkins server.`


Answers:
author: Caroline R
body: Hi, [@Sarath Nagarajan](/t5/user/viewprofilepage/user-id/4640457), thank you for reaching out to Atlassian Community.

Could you please add **Debug: "true"** in the Pipe configuration and share the output with us? This will help us to get more logs that can help us to investigate the issue further.

Please feel free to share any additional information regarding this case.

Kind regards,   
Caroline

comments: author: Sarath Nagarajan
body: Hello Caroline R

the issue got somehow fixed on its own. After multiple attempts of running the pipeline from BB.

Thanks for your response.


author: Caroline R
body: Hi, [@Sarath Nagarajan](/t5/user/viewprofilepage/user-id/4640457),

Thanks for the update! I'm glad to know everything is working now. Please let us know in case you face this problem again.

Kind regards,   
Caroline


Tags: bitbucket-cloud

bitbucket-pipelines

cloud

jenkins
Python project getting failed when we run pipeline
Asked by venkatanareshimi:

I placed the python project in bitbucket repository and prepared the pipeline for python project with default options.But when i run the pipeline getting below error.Please help me out how to solve this error.

pytest -v tests/* --junitxml=test-reports/report.xml  
============================= test session starts =======  
platform linux -- Python 3.8.12, pytest-7.0.1, pluggy-1.0.0 -- /usr/local/bin/python  
cachedir: .pytest_cache  
rootdir: /opt/atlassian/pipelines/agent/build  
collecting ... collected 0 items  
- generated xml file: /opt/atlassian/pipelines/agent/build/test-reports/report.xml -  
============================ no tests ran in 0.00s =============================  
ERROR: file or directory not found: tests/*


Answers:
author: Patrik S
body: Hello [@venkatanareshimi](/t5/user/viewprofilepage/user-id/2489162) ,

Thank you for reaching out to Atlassian Community.

The error you have reported indicates that the **tests** folder does not exist in the repository. When you execute **pytest**command, it expects to find files with tests in that directory.

In case you have your test files in a different directory in your repository, you will have to replace **tests/\*** in the command in your yml file with the path of the directory where the tests exist, like below :

    pytest -v <path to the the folder containing the tests> --junitxml=test-reports/report.xml

Hope that helps. Let us know if you have further questions.

Thanks [@venkatanareshimi](/t5/user/viewprofilepage/user-id/2489162) .

King regards,

Patrik S


Tags: bitbucket-cloud

cloud
I'm not receiving verification emails from Atlassian
Asked by Zeeshan Fareed:

I'm not receiving the confirmation Email to Zeeshan Fareed on my Bitbucket account. Email is hosted on Gmail too, so not blocked from the server. Not received anything from bitbucket.


Answers:
author: Caroline R
body: Hi, [@Zeeshan Fareed](/t5/user/viewprofilepage/user-id/4770894), welcome to the community!

I checked our logs and confirmed that your email had a block on the server that prevented emails from being sent to you. So I removed your email from this suppression list.

Could you please confirm if you receive the emails now?

Kind regards,  
Caroline

comments: author: Zeeshan Fareed
body: Hi Caroline R,  

Thank you for your quick response,  

I will just let you confirm shortly.  

Thank you


author: Zeeshan Fareed
body: Hi [@Caroline R](/t5/user/viewprofilepage/user-id/3934006) ,  

Thank you for your efforts.  

I got the invitation email now.  

Thank You :)


author: Caroline R
body: Hi, [@Zeeshan Fareed](/t5/user/viewprofilepage/user-id/4770894), thanks for the confirmation! I'm glad to know everything is working fine now.

Kind regards,   
Caroline


author: Zeeshan Fareed
body: I was received the emails when i previously added, but after removing my this account, it unable to invite again on bitbucket, i think my email is in the grey/blacklist, and need to be removed from there, then i hope, i will be able to get emails like of invitation emails.  

Thank you.


Tags: bitbucket-cloud

cloud
How to merge changes to different branches without previous merges
Asked by Murat G?r:

We have two branches

* develop
* master

We are working on the "develop" branch with PR. Each developer gets "pull" from the "develop" branch and creates a new branch let's say feature/item-1 and merges back to the "develop" with PR and at least 1 approval rule. This works fine.

After that, we deploy the "develop" branch to our testing servers so the QA team can test if the development is ok or not.

What we trying to figure out: After a branch that is merged, tested, and accepted by the QA, we want to merge this branch into the "release" branch but without getting all the differences between "development" and "release" branches. Right now if we crate the PR "feature/item-1" branch into the "release" branch it includes the past commits from the "develop" branch which we don't want because it includes the commits not tested.

We may use cherry-pick the branch into "release" but and the end of the day we are using bitbucket and there must be a solution, right? :D


Answers:
author: Caroline R
body: Hi, [@Murat G?r](/t5/user/viewprofilepage/user-id/4099926), thank you for reaching out to Atlassian Community.

Usually, when using git/pull requests, we would only merge in branch/commits into the 'develop' branch after it is tested, rather than merging everything into a singular branch to then be tested at that point. This would allow you to only have good/valid commits in the develop branch, meaning that you can then merge from that branch to main whenever you're ready to build/publish the changes as a new version of the application.

To give you some context, with git in general, the idea is to keep branches healthy by only merging once you know content is ready. Merging any commits/branches into a universal testing branch isn't a common practice and isn't something we often see so unfortunately we don't have any tools or common methods to help guide you with your workflow as it exists today (except cherry-pick as you mentioned).

With this in mind, we typically see developers pushing to branches with a specific pattern like "feature/name-of-feature" so that the pattern of "feature/\*" can be tested against with the same build/test phase as discussed in [this article](https://support.atlassian.com/bitbucket-cloud/docs/use-glob-patterns-on-the-pipelines-yaml-file/). I would also like to suggest that you take a look at [Git Feature Branch Workflow](https://www.atlassian.com/git/tutorials/comparing-workflows/feature-branch-workflow) and check if this workflow could help you and your team.

I hope this helps, but do let me know if you have any questions.

Kind regards,   
Caroline


Tags: bitbucket-cloud

cloud

git

merge
I can't request bitbucket rest api with right username and password, and the status code is 403.
Asked by yue wang:

hello!

when I use bitbucket rest api like <https://api.bitbucket.org/2.0/repositories/{workspace}/> to get repositories, the return status code is 403 and content is 'b'Too many invalid password attempts. Log in at <https://id.atlassian.com/> to restore access.\\n''.

But my username and password is right , I can use them login <https://id.atlassian.com/> through broswer.

I use python package requests do my request, the code like this:

```
from requests.auth import HTTPBasicAuth
import requests

username = "{username}"
password = "{password}"
email = "{email}"
worksapce = "{worksapce}"
BITBUCKET_URL = "https://api.bitbucket.org/2.0"
BITBUCKET_AUTH = HTTPBasicAuth(username, password)
BITBUCKET_HEADERS = {"content-type": "application/json"}

response = requests.get(f"https://api.bitbucket.org/2.0/repositories/{worksapce}/",
                        params={
                            "pagelen": 100
                        },
                        auth=BITBUCKET_AUTH,
                        headers=BITBUCKET_HEADERS)

print(response.status_code)

print(response.content)
print(response.json())
```

please help me! Any help would be highly appreciated.

Thanks in advance!


Answers:
author: Ben
body: Hey Yue!

The error which you have specified indicates to me that Git is unable to authenticate the password associated with the user.  
I have some suggestions:

1. Reset the password associated with the account if you intend to use regular username/password basic auth **(this is being deprecated on 01/03/22)** : <https://id.atlassian.com/login/resetpassword>
2. If this does not work, instead of using the normal account password can you try setting up an **App Password** and replacing the basic password with the app password?  
   <https://support.atlassian.com/bitbucket-cloud/docs/app-passwords/>
3. To set up the **App Password** , you can navigate to the account settings here once logged into that account - <https://bitbucket.org/account/settings/app-passwords/>  
   You can create the **App Password** and give it the permissions it needs accordingly.

-  
If the regular password has been changed instead (option 1), please ensure it is cleared from any applications/GIT clients, keychain access (Mac), credential manager (Windows), deleted from /etc/shadow directory (Linux).  
Let me know if this helps.  
**- Ben (Bitbucket Cloud Support)**

comments: author: yue wang
body: Thank you for your help! Your second resolution can work, first not!

Thank you again!


Tags: bitbucket-cloud

cloud
how to integrate sonarQube with bitbucket pipeline creation
Asked by Krishnai Shrikant Jirange:

After adding code in bitbucket yaml. I am not able to build that code


Answers:
author: Ajay _view26_
body: Hi [@Krishnai Shrikant Jirange](/t5/user/viewprofilepage/user-id/4771053)

Welcome to the community!

Can you add logs or the yaml file for the community members to help you out?

Cheers

Ajay

comments: author: Krishnai Shrikant Jirange
body: ---  
image: "mcr.microsoft.com/dotnet/core/sdk:3.1"  
pipelines:  
branches:  
Masterbranch:  
-  
step:  
script:  
-  
pipe: "sonarsource/sonarqube-scan:1.0.0"  
variables:  
SONAR_HOST_URL: ""  
SONAR_TOKEN:   

-  
step:  
artifacts:  
- publish/Core_HelloWorld.zip  
caches:  
- dotnetcore  
name: Package  
script:  
- "apt-get update"  
- "apt-get install zip -y"  
- "dotnet build"  
- "dotnet publish ./Core_HelloWorld/Core_HelloWorld.csproj -c Release -o ./publish"  
- "cd ./publish"  
- "zip -r Core_HelloWorld.zip ."  
-  
step:  
deployment: test  
name: "Deploy to test"  
script:  
-  
pipe: "microsoft/azure-web-apps-deploy:1.0.3"  
variables:  
AZURE_APP_ID:   
AZURE_APP_NAME: BBWEBAPP-dev  
AZURE_PASSWORD:   
AZURE_RESOURCE_GROUP: BBPOC-dev  
AZURE_SUBSCRIPTION_ID:   
AZURE_TENANT_ID:   
ZIP_FILE: publish/Core_HelloWorld.zip  
trigger: manual  
default:  
-  
step:  
caches:  
- dotnetcore  
name: "Build and Test"  
script:  
- "dotnet restore"  
- "dotnet build"  
- "dotnet test"

In Above code only azure values are not visible here but I have used in my original file.


Tags: bitbucket-cloud

cloud
we have a repo in BB, Who can access the repo, who can clone it, edit , As a admin how to identify
Asked by C Chenna:

we have a repo in Bitbucket, want to know that who can access the repo, who can clone it, who can edit it , As a admin from where we can get this details.

thanks in advance


Answers:
author: Vishwas
body: [duplicate](https://community.atlassian.com/t5/Bitbucket-questions/Bitbucket-Permission-issue/qaq-p/1951586)


Tags: bitbucket-server

server
Bitbucket Permission issue
Asked by C Chenna:

we have a repo in Bitbucket, want to know that who can access the repo, who can clone it, who can edit it , As a admin from where we can get this details.

thanks in advance


Answers:
author: Fabio Racobaldo _Herzum_
body: Hi [@C Chenna](/t5/user/viewprofilepage/user-id/4579133) ,

you can check project and repo permissions in order to retrieve all these information ([Using repository permissions](https://confluence.atlassian.com/bitbucketserver/using-repository-permissions-776639771.html#:~:text=Repository%20permissions%20in%20Bitbucket%20Data,already%20granted%20from%20project%20permissions.&text=Go%20to%20Settings%20%3E%20Permissions%20for%20the%20repository.))

Read -\> can access and clone repo

Write -\> can access, clone ad edit

I know that if access is based on groups, it is not so clear retrieve info based on users. For this reason I developed my own data center plugin to retrieve all these info per users basis.

Hope this helps,

Fabio


author: C Chenna
body: Thank You [@Fabio Racobaldo _Herzum_](/t5/user/viewprofilepage/user-id/781528)

comments: author: Fabio Racobaldo _Herzum_
body: you're welcome [@C Chenna](/t5/user/viewprofilepage/user-id/4579133)


Tags: bitbucket-server

server
Need git gc on remote repository
Asked by lwallace:

Hello,

I have a private repository on an academic plan that has hit the 4GB size limit and I am unable to reduce the size with the options described at the suggested <https://confluence.atlassian.com/x/xgMvEw> link. I have tried enabling the Labs feature and reset with the force push (the latter of which has worked for me in the past, but did not work this time). The repository in question is bitbucket.org/nr\*ec\*/ec\*nb\*\*_\*ar, please assist.

Thank you,

Lauren


Answers:
author: Ben
body: G'day!

I've successfully run garbage collection against your remote repository (**nr\*ec\*/ec\*nb\*\*_\*ar** ) in the back-end to clean up any dangling commits.  

The repository size has reduced from 1.8GB and is now currently 139.2MB.  

Would it be possible for you to check it on your end (by navigating to your **Repository \> Settings** ) and see if that has helped?  

We want to inform you that we do have a Feature request: <https://jira.atlassian.com/browse/BCLOUD-11593> to provide the option to run the GC from the end-user GUI. This way you need not raise a ticket and wait for the support person to run the GC on your behalf.  

Our Dev team is currently working on implementing the feature request and we don't have any ETA for the fix. I would suggest you "Watch" this ticket for future updates from our Dev team.  

Hope it helps.  
Let me know how it goes.

- Ben (Bitbucket Cloud Support)


author: Caroline R
body: Hi, Lauren, thank you for reaching out to Atlassian Community.

I ran the GC against your repository and managed to reduce its size to 259.9 MB.

I also would like to share with you that we have a feature request to allow users to mark repositories for git GC, as you can check here:

* <https://jira.atlassian.com/browse/BCLOUD-11593>

Please consider adding yourself as a watcher to receive the updates as we make progress with this. If you are not familiar with our Feature Request Policy, you can read more about it [here](https://confluence.atlassian.com/support/implementation-of-new-features-policy-201294576.html).

Feel free to share any additional questions or concerns regarding this case.

Kind regards,   
Caroline

comments: author: lwallace
body: Thank you very much Caroline! I had actually upvoted the request you mention some time ago and signed up to receive notifications on the issue because this affects a couple of our repos, it would be great if a manual git gc feature could be implemented!


Tags: atl-rvw

bitbucket-cloud

cloud
Why BitBucket Pipelines Caches not caches dotfiles on root folder
Asked by xicond:

Hi,

I planned to saved a commit ID in cache so that I know the cache point

like:

```
git rev-parse HEAD > vendor/.commit
```

<br />

then I put cache definition like

```
definitions:
  caches:
    vendor: vendor
```

But seems the .commit not found on next pipeline execution, is that the expected behavior ?


Answers:
author: xicond
body: Sorry, my mistake on command

Some of my step mistakenly put in wrong folder


Tags: bitbucket-cloud

bitbucket-pipelines

cache

cloud
BitBucket Group Repos & Permissions API
Asked by Kristin Lyons:

I'm looking to get an API query I can run that will show me a list of the groups with the user membership, the repositories and the repository permissions. I am using Postman with this GET {{baseUrl}}/workspaces/**workspacename**/permissions/repositories?page=20\&pagelen=100

It works great but it has over 3k results. I think it'd be easier if I can get a list of groups with their repository permissions and then the users' group membership.

![Screen Shot 2022-02-21 at 4.20.04 PM.png](https://community.atlassian.com/t5/image/serverpage/image-id/184619i7EDDC789D855586A/image-size/large?v=v2&px=999 "Screen Shot 2022-02-21 at 4.20.04 PM.png")![Screen Shot 2022-02-21 at 4.20.16 PM.png](https://community.atlassian.com/t5/image/serverpage/image-id/184620i3CB204E70F05F652/image-size/large?v=v2&px=999 "Screen Shot 2022-02-21 at 4.20.16 PM.png")


Answers:
author: Caroline R
body: Hi, [@Kristin Lyons](/t5/user/viewprofilepage/user-id/1032864), thank you for reaching out to Atlassian Community.

We do have groups and group-privileges endpoints that could be useful to you. Just to give you some context around our API, our old rest API 1.0 used to include endpoints that would allow these sorts of operations, however, the [1.0 API has been deprecated](https://developer.atlassian.com/cloud/bitbucket/deprecation-notice-v1-apis/) with the intent that the 2.0 API would be a direct replacement.

With that said, there are a few old 1.0 endpoints that we kept in place as a temporary solution until the 2.0 replacements are made available.

Until the Atlassian platform services are fully available in Bitbucket, we will continue to support these 1.0 REST endpoints:

    /1.0/groups/1.0/group-privileges/1.0/invitations/1.0/users/{accountname}/invitations

You can find all the information about these endpoints here:

* [Use Bitbucket REST API version 1](https://support.atlassian.com/bitbucket-cloud/docs/use-bitbucket-rest-api-version-1/)

* [group-privileges Endpoint](https://support.atlassian.com/bitbucket-cloud/docs/group-privileges-endpoint/)

* [groups Endpoint](https://support.atlassian.com/bitbucket-cloud/docs/groups-endpoint/)

I hope this helps, but do let me know if you have any questions.

Kind regards,   
Caroline


Tags: api

bitbucket-cloud

cloud
Old Repositories Missing From Account
Asked by Andrew:

Hi, after logging into Bitbucket, I'm not able to see / access any of my old private Git repositories from a few years ago that were stored there. Trying to fetch / push from my local copy returns a "Permission denied" / "fatal: Could not read from remote repository" error. How can I regain access to all of my old repositories? I checked my email and never received any notice that my access to these repositories would be changing or that the repositories would go away.

Thanks in advance.


Answers:
author: Ben
body: Hey Andrew!

I have attempted to locate your details so that I can access your workspace and provide assistance but these are not shared.   
Would you please provide your **workspace ID** (ie the workspace that appears in your URL **<https://bitbucket.org/WORKSPACENAME>**) if you are comfortable sharing this, given that the comment thread is public?

Thank you.

- Ben (Bitbucket Cloud Support)

comments: author: Andrew
body: Hey [@Ben](/t5/user/viewprofilepage/user-id/4537226), thanks for getting back to me. Could I share this with you over a more private channel with you so that we can get this resolved?


author: Ben
body: Hi [@Andrew](/t5/user/viewprofilepage/user-id/4769907) !

I have raised a support ticket on your behalf, you will see this in your inbox for your registered email address. Please provide the workspace ID which you are encountering the issue with in your reply to the ticket that has been raised in your email inbox.

Thank you,

- Ben (Bitbucket Cloud Support)


author: Andrew
body: Appreciate it [@Ben](/t5/user/viewprofilepage/user-id/4537226) ! I'll respond there.


Tags: bitbucket-cloud

cloud