- 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
...map") no points are displayed: https://genenetwork.org/show_trait?trait_id=NM_029911&dataset=UTHSC_BXD_WB_RNASeq1112
# Tags:
* source: robwwilliams
* type: mapping user interface display failure...
- Designing an issue tracker on gemini
✓ issue opened on Jul 25 2021 by Pjotr Prins, last updated on Feb 02 2022 by Pjotr Prins
...an issue tracker on gemini
Why do we want to consolidate issue trackers and kanban boards using gemini+git? Several reasons:
* Get rid of external web service dependencies (in our case github issue...
- 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
...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 for the mapping figure.
# TODO
[X] Display track showing...
- 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
...does not match the observed issue.
## TODO
* [ ] Test in a similar environment to the CD environment to replicate the issue.
* [ ] Investigate the internals of the QTL library for any unintended `rm`...
- Sheepdog
issue opened on Nov 08 2021 by Pjotr Prins, last updated on Jul 01 2022 by Arun Isaac; 3 of 17 tasks done
...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/group after backup...
- 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
...EC2 URL
* [X] Disable GN mailing list URL
=> ./gn1-pairscan.gmi [x] Pairscan not working
=> ./gn1-network-graph.gmi [X] Fix network graph (it does not display image)
* [ ] Disable all defunct URLs
- Capture state of phenotypes in a HASH
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
...a dataset - i.e. the column one uses for mapping. @zsloan this is metadata and I suggest we use RDF so we can have a historic view of changes in datasets. A change can be described as table - mapped...
- 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
...fine.
## 413 Request Entity Too Large (fixed)
On mapping from
=> https://fallback.genenetwork.org/show_trait?trait_id=10002&dataset=HET3-ITPPublish
This resolved itself - probably a permission issue.
- 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...
- 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
...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 the machine. The backups are...
- 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...
- 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?
- 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/...
- Allow analyses to be done between traits from "individuals" groups and their corresponding "main" group
issue opened on Jul 21 2022 by Zachary Sloan
These mappings could be stored in a simple JSON file.
The "main" group trait(s) could then have their sample data converted to the sample list of the "individuals" group, provided the mappings...
- 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
...tissue, edit issue
## Description
Add an `Edit Issue` link on each issue that drops the user in the forge's (currently GitHub) editting mode for the selected file.
For an example of what is expected...
- Enable all DataTables to call the same code
issue opened on Jul 26 2022 by Zachary Sloan, last updated on Jul 27 2022 by Zachary Sloan
...can override the defaults
Converted tables:
[X] - Search Results
[X] - Collection View
[X] - Collection List
[X] - Correlation Results
[X] - Global Search
[X] - Trait Page Sample Table
[X] - Mapping...
- Annotation
issue opened on Sep 14 2022 by Pjotr Prins, last updated on Mar 14 2023 by Arun Isaac; 0 of 5 tasks done
...mapping, architecture
# TODO
* [ ] Point out where annotation is used in code (@zsloan)
* [ ] Come up with a storage model to replace the existing Mariadb tables (pjotrp, aruni)
* [ ] Implement...
- Fix GN1 Network Graph
issue opened on Sep 15 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...that
displays the graph itself
652: body += ''' <p>This graph took %s seconds to generate with the <a href="http://www.research.att.com/sw/tools/graphviz/" class="normalsize" target="_blank">...
- AI UI Enhancements
issue opened on Mar 01 2024 by Pjotr Prins; 0 of 3 tasks done
...This issue addresses user feedback received during the testing phase of GNQA on CD. The following improvements are required
## Tasks
* [ ] Only show the link when a user is logged in - they can't use...
- Wrong CSV in ITP_10001 longevity dataset
✓ issue opened on Apr 11 2022 by BonfaceKilz, last updated on Apr 12 2022 by BonfaceKilz
...issue
- [X] Check if database is affected in any way
- [X] Send a patch to fix
- [X] Notify every relevant user
- [X] Update case-attr page with links
## Notes
### Mon 11 Apr 2022 13:19:14 EAT:
The...
- 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
...wrong.
Use the console bar of the browse to see what JS error you get.
If you get CORS errors it is because you are using a server that is not genenetwork.org and this is usually a configuration issue.
- Parsing genotyfiles
issue opened on Jul 11 2023 by Alexander_Kabui
...identify
the file in the GENOTYPE_FILES and extract sample_listx
for entire parsing code refer to:
=> https://github.com/genenetwork/genenetwork3/blob/main/gn3/db/genotypes.py
* Linked to issue...
- 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 layout is broken on certain browser versions.
This issue was reported to occur for **Firefox Version 128.3.1** ESR Version.
The root cause of the problem is unclear,
but after reviewing...
- 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...
- 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...
- 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...
- 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
...per* service. Otherwise updates are impossible.
In time we may move to hosting these services in a guix system container (a VM).
Currently there are a bunch of shepherd services (on tux02, as user...
- 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.
- Apps
issue opened on Nov 19 2024 by Pjotr Prins, last updated 5 weeks ago by Pjotr Prins; 33 of 74 tasks done
.../etc/systemd/system# cat bnw-app-container.service
[Unit]
Description = Run genenetwork BNW app container
[Service]
ExecStart = /usr/local/bin/bnw-app-container
[Install]
WantedBy = multi-user.target...