- Zoomed mapping result are empty for certain traits
issue opened on Apr 11 2022 by Zachary Sloan, last updated on Apr 13 2022 by Zachary Sloan
...robwwilliams
* type: mapping user interface display failure
* assigned: zachs
* keywords: bug
* status: in progress
* priority: high
This issue appears to be caused by marker namees being duplicated.
- Designing an issue tracker on gemini
✓ issue opened on Jul 25 2021 by Pjotr Prins, last updated on Feb 02 2022 by Pjotr Prins
...flexible, but common ones are
* request
* bug
* critical bug
* enhancement
* in progress
* testing
* later
* documentation
* help wanted
* closed
the keyword statement may have aliases, such as tag...
- GN1 Production
issue opened on Sep 15 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi; 3 of 8 tasks done
...bug
* priority: critical
* keywords: GN1
* status: in progress
* kanban: pjotrp
* assigned: pjotrp, zachs, robw
## List of outstanding issues
(see also E-mail Rob 14 Sep 2021)
* [ ] Fix annotating...
- Fallbacks and backups
issue opened on Aug 31 2021 by Pjotr Prins, last updated on Jun 28 2024 by Pjotr Prins; 3 of 25 tasks done
.../backup/tux01/borg-genenetwork::TUX01_BORG_GN2_HOME-20210830-04:00-Mon
```
## Get backups running on fallback
Recently epysode was reinstated after hardware failure. I took the opportunity to reinstall...
- Annotate traits page with metadata from RDF
✓ issue opened on Sep 30 2022 by Munyoki Kilyungi, last updated on Dec 15 2022 by Munyoki Kilyungi; 16 of 16 tasks done
...patches for review
## Display the metadata in GN2 as HTML
* [x] Display the metadata as part of GN2 web-page. This data is stored as HTML. How do work around this WRT displaying in a UI friendly way?
- Investigate and Fix `rm` Command in `rqtl` Logs
issue opened on Jan 08 2025 by Alexander_Kabui, last updated on Jan 09 2025 by Munyoki Kilyungi; 4 of 6 tasks done
...Bug
* status: in progress
* keywords: external, qtl, rqtl, bug, logs
## Description
For QTL analysis, we invoke the `rqtl` script as an external process through Python's `subprocess` module.
For...
- Wrong CSV in ITP_10001 longevity dataset
✓ issue opened on Apr 11 2022 by BonfaceKilz, last updated on Apr 12 2022 by BonfaceKilz
...bug
* status: closed
* priority: critical
* keywords: critical bug, in progress, metadata, phenotypes
## Description
[From Suheeta]:
"I downloaded the sample csv file for ITP_10001 to add a couple...
- Sheepdog
issue opened on Nov 08 2021 by Pjotr Prins, last updated on Jul 01 2022 by Arun Isaac; 3 of 17 tasks done
...sheepdog_rsync.rb - test for 'total size is 0'
* [ ] sheepdog_list tag and filter switches improve behaviour
* [ ] add sheepdog_web_monitor - currently using plain curl
* [X] borg: set user/...
- GN1 github problem
issue opened on Dec 17 2022 by Pjotr Prins
...rm --cached --ignore-unmatch \
MouseTissuesRWWMay08.xls' --prune-empty --tag-name-filter cat -- --all
git reflog expire --expire=now --all && git gc --prune=now --aggressive
```
Note this rewrites...
- AI UI Enhancements
issue opened on Mar 01 2024 by Pjotr Prins; 0 of 3 tasks done
AI UI Enhancements
## Tags
* Assigned: alexm, shelbys
* Keywords: UI, GNQA
* Type: critical
* Status: In Progress
## Description
This issue addresses user feedback received during the testing phase...
- 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
...logging in, rather than sending them to the homepage. Additionally, display the message "You are required to log in" on the current page instead of on the homepage.
## Tasks
* [x] Redirect users...
- Fallback issues
issue opened on Mar 22 2024 by Pjotr Prins, last updated on Apr 05 2024 by Pjotr Prins; 3 of 6 tasks done
...type: bug
* assigned: pjotrp
* keywords: systems, fallback, deploy
* status: in progress
* priority: critical
# Tasks
* [X] 502 timeout errors
* [X] Rqtl2 not working
* [X] 413 error
* [ ] BNW error...
- Search results presentation
issue opened on Apr 04 2023 by Alexander_Kabui
...displayed in tabular form and too many columns are presented to user overlapping the page
Design should be simple and eye catching to user
links to suggesetd designs:
=> https://www.ncbi.nlm.nih.gov/...
- 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
TODO
[X] Display track showing homology across mouse/human/maybe rat (done for mouse, won't be hard to also enable for other species)
[ ] Make it display an arrow depending on the strand (whether...
- Fix GN1 Network Graph
issue opened on Sep 15 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...bug
* priority: high
* keywords: GN1, Network Graph
* status: in progress
* kanban: pjotrp
* assigned: pjotrp, zachs
## Tracking
To reproduce this bug: select a 'shopping basket' and click on network...
- Search results for SNP looks weird
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Oct 12 2022 by Munyoki Kilyungi
...past:
=> https://user-images.githubusercontent.com/11820306/82554424-8e0ac600-9b6e-11ea-9a50-f53506eb44a5.png Screen Shot 2020-05-20 at 10 01 10 PM
Here's how it looks like now:
https://user-images...
- Slow query
issue opened on May 27 2023 by Pjotr Prins, last updated on May 29 2023 by Pjotr Prins; 0 of 2 tasks done
...it shoud not be critical here. Though I found
BUFFER CACHING:
The InnoDB Buffer Pool caches data and index pages. MyISAM only caches index pages.
Just in this area alone, MyISAM does not waste time...
- Each shepherd service needs its own guix profile.
issue opened on Nov 03 2021 by Efraim Flashner, last updated on Jun 21 2024 by Pjotr Prins
It is
used to fire up a guix shell/environment:
* bnw
* cronjob-gitea
* cronjob-pubmed (genecup)
* genecup
* gitea
* ipfs
* power
* rn6app
* singlecell
## Tags
* assigned: efraim, pjotrp
* type: bug...
- Fix Broken Global Search UI
issue opened on Jan 07 2025 by Alexander_Kabui, last updated on Jan 07 2025 by Alexander_Kabui; 0 of 2 tasks done
...search, UI, bug, Refactor
* Type: UI, bug
## Description
The Global search UI layout is broken on certain browser versions.
This issue was reported to occur for **Firefox Version 128.3.1** ESR...
- GN Markdown Editor Integration
issue opened on Jun 07 2024 by Alexander_Kabui, last updated on Aug 22 2024 by Alexander_Kabui; 9 of 10 tasks done
...user, in our case from auth)
* `commit_message`
If the request succeeds, the response should be:
```json
{
"status": "201",
"message": "Committed file successfully",
"content": "Test for new user\n...
- Marker covariates implemented wrong in rqtl_wrapper.R
issue opened on Sep 22 2021 by Zachary Sloan, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...in rqtl_wrapper.R is wrong. For the time being,
I've removed this option. Currently just waiting on Danny to get back to me with the fix (which I'll then add to rqtl_wrapper.R)
## Tags
* type: bug...
- Using guix-bioinformatics in a channels.scm file
issue opened on Aug 15 2021 by Efraim Flashner, last updated on Oct 09 2022 by Pjotr Prins
...-bioinformatics git server that is *not* gitlab or github.
I think we should move to ssh keys and cgit. The latter has to run in a container, ideally.
## Tags
* assigned: efraimf, pjotrp
* type: bug...
- Return canned text if notebook description returns none
issue opened on Oct 28 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
Return canned text if notebook description returns none
## Tags
* type: bug
* assigned: jgart
* priority: high
* status: in progress
* keywords: binderlite, notebooks
## Description
Notebooks that do...
- Integrate styling of app with GN2
issue opened on Oct 28 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...bug
* priority: medium
* keywords: binderlite, notebooks, styling, UI
## Description
Currently using antiweb for styling with modifications.
=> https://git.sr.ht/~sircmpwn/antiweb antiweb
Copying nav...
- Troubleshoot response inconsistencies for GN-llm
issue opened on Jan 10 2024 by Alexander_Kabui
...responses take too long, and related queries with differing sentence structures may result in no response. There is a need to rethink how we handle polling to the Fahamu API to prevent users...
- Gn Markdown Editor implementation
issue opened on Aug 07 2023 by Alexander_Kabui, last updated on Sep 11 2023 by Alexander_Kabui; 4 of 5 tasks done
...Markdown Editor implementation
### Notes
Gn renders multiple markdown pages as html,the idea of this project is to allow users to edit and live preview the results
also added to this is the ability...
- 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
...that drops the user in the forge's (currently GitHub) editting mode for the selected file.
For an example of what is expected, see the `edit page` link/button at
=> http://gemini.thebird.nl/gemini/...
- Tux02 Production
issue opened on Oct 07 2021 by Pjotr Prins, last updated on Dec 14 2022 by Pjotr Prins; 17 of 22 tasks done
...ports (nginx)
* [?] set up network for external tux02e.uthsc.edu (128.169.4.52)
* [X] set up deployment evironment
* [X] sheepdog copy database backup from tux01 on a daily basis using ibackup user...
- Branding and front-end-services
issue opened on Jun 14 2023 by Pjotr Prins; 0 of 1 tasks done
...of users operating at the same time. Its main challenge is running long operations while still being able to serve others.
The ultimate goal is increased flexibility in creating front-ends and portals.
- GN2 Time Machines
issue opened on Aug 19 2022 by Pjotr Prins, last updated on Sep 05 2022 by Alexander_Kabui; 4 of 10 tasks done
.../blog/2013/08/20/why-is-the-ibdata1-file-continuously-growing-in-mysql/
(obviously we don't want to use mysqldump right now, but I'll need to do some future work).
### Setting up GN2
Create a gn2 user...
- Apps
issue opened on Nov 19 2024 by Pjotr Prins, last updated 5 weeks ago by Pjotr Prins; 33 of 74 tasks done
...[Service]
ExecStart = /usr/local/bin/bnw-app-container
[Install]
WantedBy = multi-user.target
```
We need to make sure the garbace collector does not destroy the container, add the --root switch...