- Feature Request: Create Test Accounts
issue opened on Sep 16 2024 by Frederick Muriuki Muriithi, last updated on Sep 17 2024 by Frederick Muriuki Muriithi
Feature Request: Create Test Accounts
## Tags
* assigned: fredm, alex
* status: open
* type: feature request, feature-request
* priority: medium
* keywords: gn-auth, auth, test accounts...
- Add convenience templates
✓ issue opened on Oct 28 2021 by jgart, last updated on Jul 11 2022 by Arun Isaac
I was thinking of an interface like the following:
```
gnbug report feature-request "New feature: IPFS Downloads"
```
Or expressed as generic command parameters:
```
command subcommand tag(s) title...
- Pass on Unknown GET Parameters
issue opened 3 weeks ago by Frederick Muriuki Muriithi
...has to them manually set them up again. This, while not a big deal, is annoying and wastes a few seconds each time.
This feature request proposes to pass any unknown GET parameters untouched through...
- Prevent Weak Passwords
issue opened on Feb 27 2024 by Frederick Muriuki Muriithi, last updated 3 weeks ago by Frederick Muriuki Muriithi
...feature-request, feature request
## Description
=> https://matrix.to/#/!mBYtTotZGiPpHmjJnI:matrix.org/$yaw0uk-JyHGBC8Jw-b2I1VhGoaWwNEO_eOiSAO8RSDs?via=matrix.org
> pjotrp
> how do we prevent weak...
- Replace Redis with SQL
issue opened on Mar 12 2025 by Frederick Muriuki Muriithi, last updated 3 weeks ago by Frederick Muriuki Muriithi
...feature-request, feature request
* keywords: gn-uploader, uploader, redis, sqlite, sqlite3
## Description
We currently (as of 2024-06-27) use Redis for tracking any asynchronous jobs (e.g. QC...
- Provide Page/Link for/to Uploaded Data
✓ issue opened on Jul 10 2024 by Frederick Muriuki Muriithi, last updated on Oct 14 2025 by Frederick Muriuki Muriithi
...feature, feature request, feature-request
* keywords: gn-uploader, uploader, data dashboard
## Description
Once a user has uploaded their data, provide them with a landing page/dashboard for the data...
- Add a transient interface for tissue
✓ issue opened on Mar 28 2022 by BonfaceKilz, last updated on Jul 08 2022 by Arun Isaac
...feature-request
* keywords: linter, tissue
* assigned: bonfacem
* priority: low
## Description
Add a transient interface for GNU Emacs for tissue. Check out transient:
=> https://github.com/magit/...
- gn-uploader: Resume Upload
✓ issue opened on Jun 24 2024 by Frederick Muriuki Muriithi, last updated on Jul 03 2024 by Frederick Muriuki Muriithi; 4 of 4 tasks done
...flisso
* type: feature request, feature-request
* keywords: gn-uploader, uploader, upload, resume upload
## Description
If a user is uploading a particularly large file, we might need to provide...
- Link Authentication/Authorisation
✓ issue opened on Jun 24 2024 by Frederick Muriuki Muriithi, last updated on Oct 14 2025 by Frederick Muriuki Muriithi
...critical
* type: feature request, feature-request
* keywords: gn-uploader, gn-auth, authorisation, authentication, uploader, upload
## Description
The last chain in the link to the uploads is...
- Send out Confimation Emails on Registration
✓ issue opened on Feb 27 2024 by Frederick Muriuki Muriithi, last updated on Sep 16 2024 by Frederick Muriuki Muriithi
...feature request, feature-request
* keywords: gn-auth, email, user registration, email confirmation
## Description
Send out a emails to confirm that the emails users provide are valid. Probably add...
- New Privileges: Samples Ordering
issue opened on Sep 19 2024 by Frederick Muriuki Muriithi
...feature-request, feature request
* keywords: gn-auth, auth, privileges, samples, ordering
## Description
From the email thread:
```
Regarding the order of samples, it can basically be whatever we...
- Enable User Masquerade
✓ issue opened on May 22 2023 by Frederick Muriuki Muriithi, last updated on May 23 2023 by Frederick Muriuki Muriithi
...feature request
## Description
To enable debug of issues, or to support some user request, we need to build in a masquerade feature to enable the system admin to masquerade as a particular user...
- Add search, select and export to datatables table
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
...feature-request
* status: unclear
* keywords: datatables, UI, low priority
## Description
=> https://github.com/genenetwork/genenetwork2/issues/439 From GitHub
### Is your feature request related...
- Sort by Attributes
✓ issue opened on May 31 2024 by Frederick Muriuki Muriithi, last updated on May 31 2024 by Zachary Sloan
...feature-request, feature request
* priority: high
* status: closed
* keywords: genenetwork2, sorting, attributes
## Description
From the email:
> This trait:
>
> https://genenetwork.org/show_trait...
- Temporary Traits Access Concerns
issue opened on Aug 03 2023 by Frederick Muriuki Muriithi
...type: feature request
* priority: medium
* status: open
* assigned: fredm, zachs
* keywords: temp traits, temporary traits, access control
## Description
The temporary traits feature allows users...
- Reset/Forgot Password Feature for GN2
✓ issue opened on May 15 2024 by Munyoki Kilyungi, last updated on Sep 16 2024 by Frederick Muriuki Muriithi
...feature-request
## Description
Should a user forget his/her password, there's no clear way to reset the password.
This issue is
=> https://git.genenetwork.org/gn-auth/tree/gn_auth/auth/authorisation/...
- Capture Data on the BXDs in RDF
✓ issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Oct 12 2022 by Munyoki Kilyungi
...feature-request, enhancement
* keywords: RDF, BXD, REST, from github, high priority
## Description
### Is your feature request related to a problem? Please describe.
We aim to capture metadata on...
- Show Last Edited
issue opened on Jul 24 2023 by Frederick Muriuki Muriithi
Show Last Edited
## Tags
* type: feature request
* priority: medium
* assigned: fredm
* keywords: editing
* status: open
## Description
Following the GNSoC Plenary meeting of Thursday, 20 July 2023...
- gnbug cat
✓ issue opened on Sep 22 2021 by jgart, last updated on Sep 28 2021 by jgart
gnbug cat
* feature-request
What do you think of having a `gnbug cat`? It is similar to `gnbug edit` but
instead of opening with your `EDITOR` it prints the given issue number to
standard output.
I...
- Implement "Refresh Token" Feature for JWTs
✓ issue opened on Apr 26 2024 by Frederick Muriuki Muriithi, last updated on Jun 26 2024 by Frederick Muriuki Muriithi
...feature-request, bug
* keywords: gn-auth, token, refresh token, jwt
## Description
We have recently moved to using JWT tokens in place of the older simpler tokens. The JWT tokens have a tiny expiry...
- Add the option to save traits uploaded with the Submit Trait option
issue opened on Jul 19 2022 by Zachary Sloan
...feature-request
* status: open, in progress
* keywords: data, meta-data
# Description
Current the Submit Trait feature only allows for trait data (submitted as just a string of values) to be saved...
- Capture state of phenotypes in a HASH
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
...feature-request
* status: in progress
* priority: medium
* keywords: phenotypes, REST, UI
## Description
=> https://github.com/genenetwork/genenetwork2/issues/551 From GitHub
To represent the state...
- Add "Target" (Y) Column in Partial Correlations Selection Table
✓ issue opened on Apr 22 2022 by Frederick Muriuki Muriithi, last updated on May 26 2022 by Frederick Muriuki Muriithi
...migration, feature-request
* status: closed, completed
* keywords: partial correlations, datatables
## Description
Currently, the partial correlations in GN2 are run against a selected dataset, and...
- GeneNetwork CLI
document created on Sep 20 2021 by jgart, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...feature-request
* priority: low
* keywords: command-line interface, CLI
## Description
It would be great for GeneNetwork to have a nice command line client for doing
most if not all the things you...
- Fix Refresh Token
✓ issue opened on Dec 05 2024 by Frederick Muriuki Muriithi, last updated on Oct 14 2025 by Frederick Muriuki Muriithi
...feature-request, bug
* keywords: gn-auth, token, refresh token, jwt
## Description
The way we currently provide the refresh token is wrong, and complicated, and
leads to subtle bugs in the clients.
- Clean up Authorisation
✓ issue opened on Nov 19 2021 by BonfaceKilz, last updated on Dec 04 2023 by Frederick Muriuki Muriithi; 4 of 4 tasks done
...completed, obsoleted
* type: feature request
### Tasks
* [x] Make user able to delete/ add extra value
* [x] Fetch complete list of samples from database and genotype file
instead of only fetching...
- Render images in tissue web output
✓ issue opened on Apr 20 2022 by Arun Isaac, last updated on Jul 06 2022 by Arun Isaac
...web output
* keywords: tissue, feature request
* assigned: aruni
Links in gemtext that point to images should render as images rather than as links. This way it will be possible to inline images...
- UI Design
✓ issue opened on Dec 01 2021 by jgart, last updated on Jul 20 2022 by Frederick Muriuki Muriithi
...our format of how your dataset should look like."
> ProbeSetID Strains ...
"Inbred Set ID 1 is the same as BXD"
> These are the strains: ...
## Tags
* assigned: fredm, jgart
* type: feature-request...
- Enumerating all QC checks
✓ issue opened on Nov 19 2021 by jgart, last updated on Jul 20 2022 by Frederick Muriuki Muriithi
ume
# Enumerating all QC checks
We need to enumerate all QC checks and platforms that we want to test against.
## Tags
* assigned: fredm, jgart, arthur
* status: closed
* type: feature-request...
- Make Partial Correlations Table Searchable
issue opened on Apr 22 2022 by Frederick Muriuki Muriithi
...feature-request
* status: pending
* keywords: partial correlations, datatables
## Description
@robw notes, correctly that the table in the "Partial Correlations" workflow, where the user selects...
- Integrate Feed Analyser
✓ issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Oct 11 2023 by Munyoki Kilyungi
Integrate Feed Analyser
## Tags
* assigned: bonfacem
* type: feature-request
* status: closed
* priority: medium
* keywords: twitter, feed analyser
## Members
* bonfacem
* robw
## Description...
- Sort gnbug issues most recent first
✓ issue opened on Jan 31 2022 by Arun Isaac, last updated on Mar 22 2022 by Arun Isaac
...issue. newest-first is useful when generating gemtext/web pages where you don't want to scroll down to see the most recent issue.
## Tags
* assigned: bonfacem
* type: enhancement, feature-request...
- Hide stale issues in gnbug
✓ issue opened on Jan 31 2022 by Arun Isaac, last updated on Mar 22 2022 by Arun Isaac
...some --all flag is passed. Stale issues are tentatively defined as those issues that have been inactive for more than 6 months.
## Tags
* assigned: bonfacem, aruni
* type: enhancement, feature-request...
- Upload Strains
✓ issue opened on Dec 06 2023 by Frederick Muriuki Muriithi, last updated on Feb 27 2024 by Frederick Muriuki Muriithi; 5 of 5 tasks done
...zachs, zsloan, acenteno
* priority: high
* type: feature-request
* keywords: QC, quality control, strains, gn-uploader
## Description
Currently, the uploader simply fails when it encounters unknown...
- Redirect Users to the Correct URL on Login for GN2
✓ issue opened on Sep 17 2024 by Alexander_Kabui, last updated on Oct 16 2024 by Alexander_Kabui; 2 of 2 tasks done
...feature-request
## Description
The goal is to redirect users to the login page for services that require authentication, and then return them to the page they were trying to access before logging...
- Fetch trait names for phenotypes
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
Fetch trait names for phenotypes
## Tags
* assigned:
* status: pending
* priority: unclear
* type: feature-request, enhancement
* keywords: phenotype, from github
## Members
* robw
* rupertoverall...
- Allow analyses to be done between traits from "individuals" groups and their corresponding "main" group
issue opened on Jul 21 2022 by Zachary Sloan
...zsloan
* priority: medium
* type: feature-request
* status: open, in progress
* keywords: data, meta-data
# Description
Currently you can't do an analysis beween traits from the "main" BXD group...
- Show "Edit" Button for All Users
✓ issue opened on Jul 24 2023 by Frederick Muriuki Muriithi, last updated on Jul 24 2023 by Frederick Muriuki Muriithi
...feature request
* assigned: fredm
* priority: high
* keywords: editing
* status: closed
## Description
Show the "Edit" button for all users, but only allow users with the appropriate permissions only...
- Delete Rejected Diffs from Database
✓ issue opened on Jul 25 2023 by Frederick Muriuki Muriithi, last updated on Jul 25 2023 by Frederick Muriuki Muriithi
...type: feature request
* status: closed
* assigned: fredm
* keywords: editing, metadata audit
* priority: high
## Description
The rejected diffs will be maintained, but will simply not be shown.
- Open notebook directly if full path to notebook file is given
✓ issue opened on Nov 04 2021 by jgart, last updated on Dec 22 2021 by Frederick Muriuki Muriithi
...full path to notebook file is given
* feature-request
* assigned: jgart
We'd like to be able launch a notebook directly if the user gives the fullpath to the notebook file.
Should we allow urls like...
- Terminal output to the browser
issue opened on Oct 28 2021 by jgart, last updated on Oct 07 2022 by Arun Isaac
...to the browser
* type: feature-request
* priority: medium
* keywords: binderlite, notebooks, ansi2html
## ansi2html
Drew Devault uses ani2html in builds.sr.ht, the continuous integration system/app...
- issues/binderlite/add-spinner-for-submit-form.gmi
✓ issue opened on Nov 10 2021 by jgart, last updated on Dec 22 2021 by Frederick Muriuki Muriithi
feature-request
* assigned: jgart
Add spinner or animation to submit form while the user waits.
## Questions
1. Do we want to use xtermjs for binderlite or something simpler/lighter like an...
- Add configuration to set server name
issue opened on Nov 10 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...feature-request
* status: unclear
* priority: high
* keywords: binderlite, notebooks, configuration
## Description
Let's use environment variables as configuration
https://flask.palletsprojects.com/...
- Use "Authorisation Code Flow" for Authentication
✓ issue opened on May 08 2023 by Frederick Muriuki Muriithi, last updated on May 22 2023 by Frederick Muriuki Muriithi
...code flow
* type: feature request, improvement
## Description
We use OAuth2 for our auth(entic|oris)ation system.
Currently, the system is making use of the "Password Grant Flow"[0] which was easy to...
- UI issues/improvements
issue opened on Jul 26 2023 by Zachary Sloan
...feature-request
## Description
Linking data from the Resource page should make it clearer that the data in question is being linked to the resource (and has already been linked to the group)
The Edit...
- Paginate Resources Page
issue opened on Jul 27 2023 by Frederick Muriuki Muriithi
...feature request
## Description
Some of the Resources have too many data items linked, which leads to the page freezing when loaded.
Pagination will help aleviate the issue in those situations.
We...
- Build Registration Page for OAuth2 Clients
✓ issue opened on Dec 22 2022 by Frederick Muriuki Muriithi, last updated on May 30 2023 by Frederick Muriuki Muriithi
...authorisation, oauth2
* type: feature request
## Description
There is a need to register the OAuth2 clients that users can use to access the GN3 service with the new auth system.
Fixed with commits...
- Add an 'Edit Issue' Link to Tissue
✓ issue opened on Mar 24 2022 by Frederick Muriuki Muriithi, last updated on Apr 15 2022 by Arun Isaac
...feature-request, enhancement
* status: open, in progress
* keywords: tissue, edit issue
## Description
Add an `Edit Issue` link on each issue that drops the user in the forge's (currently GitHub)...
- Non-Clustered and Flippable Heatmaps
document created on Oct 01 2021 by Frederick Muriuki Muriithi, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...the heatmap orientation from horizontal to vertical and vice-versa
* It should be possible to generate a heatmap with no dendrograms
## Members
* fredm
* pjotr
* zsloan
## Tags
* type: feature-request...
- Quality Control Checks
✓ issue opened on Nov 17 2021 by jgart, last updated on Jul 20 2022 by Frederick Muriuki Muriithi
Assesing Phenotypes for normality with Shapiro-Wilk Test.
11. Check for annotations file.
12. Check for CRLF.
13. Check for UTF-8 encoding.
## Tags
* assigned: fredm, jgart
* type: feature-request...
- Move Data Endpoints from GN2 to GN3
✓ issue opened on Nov 03 2023 by Frederick Muriuki Muriithi, last updated on Nov 03 2023 by Frederick Muriuki Muriithi
...feature-request
* status: closed
* keywords: API
## Description
GN3 is the API server, but currently (as of Friday 03 November 2023 at 11:11AM +03:00UTC), it does not have endpoints where one can...
- Add track for showing which regions in mouse/rat correspond to human regions to the mapping figure
issue opened on Jul 21 2022 by Zachary Sloan, last updated on Sep 14 2022 by Pjotr Prins
...feature-request
* status: open, in progress
* keywords: mapping
I currently have it displaying regions in mouse with text and a UCSC genome browser link to the corresponding human region as a track...
- Rework Resources
✓ issue opened on Sep 06 2023 by Frederick Muriuki Muriithi, last updated on Feb 27 2024 by Frederick Muriuki Muriithi; 2 of 3 tasks done
...refactor, feature request, design change
* keywords: auth, authorisation, resources, design change, gn-auth
## Description
The authorisation system uses the idea of "Resources" as its most basic...
- Quality Control Project
✓ issue opened on Nov 19 2021 by Arthur Centeno, last updated on Jul 20 2022 by Frederick Muriuki Muriithi
...run from R and Python and Jupyter notebooks. Make it part of GN3.
The tricky part is still how the data is handled in escrow.
## Tags
* assigned: fredm, jgart
* priority: high
* type: feature-request...
- Export Uploaded Data to LMDB and RDF Stores
issue opened on Nov 03 2023 by Frederick Muriuki Muriithi, last updated on Oct 20 2025 by Frederick Muriuki Muriithi; 0 of 6 tasks done
...feature-request
* status: open
* keywords: API, data upload, gn-uploader
## Description
With the QC/Data Upload project nearing completion, and being placed in front of the initial user-testing...
- Migrate User Accounts from Redis to new Auth DB
✓ issue opened on Dec 22 2022 by Frederick Muriuki Muriithi, last updated on May 22 2023 by Frederick Muriuki Muriithi
...feature request
## Description
After some discussion, this issue was deemed unnecessary.
Users will have to register anew and their access details reconfirmed.
--------------------
Currently, on GN2...
- Quality Control of Data in Uploaded R/qtl2 Bundles
✓ issue opened on Feb 02 2024 by Frederick Muriuki Muriithi, last updated on Sep 16 2024 by Frederick Muriuki Muriithi; 10 of 15 tasks done
...feature request
* priority: medium
* keywords: quality control, QC, R/qtl2 bundle
## Description
Currently (2024-02-02T05:41+03:00UTC), the code simply allows the upload of data, doing the bare...
- A linter for gnbug
✓ issue opened on Oct 28 2021 by jgart, last updated on Jul 06 2022 by Arun Isaac
...feature-request
* keywords: gnbug, linter, tissue
* assigned: ??
* priority: low
* status: under discussion
## Description
Should gnbug have a linter?
For example, If a user forgets to add a tag or...
- Uploading Samples
issue opened on Sep 18 2024 by Frederick Muriuki Muriithi, last updated on Sep 19 2024 by Frederick Muriuki Muriithi
...feature-request
* keywords: gn-uploader, uploader, samples, strains
## Description
This will track the various notes regarding the upload of samples onto GeneNetwork.
### Sample Lists
From the email...
- Handling Tissue in Uploader
✓ issue opened on Mar 28 2024 by Frederick Muriuki Muriithi, last updated on Oct 15 2025 by Frederick Muriuki Muriithi; 2 of 2 tasks done
...type: feature-request
* keywords: gn-uploader, tissues, archived
## Description
"ProbeSet" studies in GeneNetwork seem to be linked to a specific tissue:
```sql
MariaDB [db_webqtl]> DESC ProbeFreeze...