- 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 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...
- BXD102xBXD077F1 Error
✓ issue opened on Mar 22 2022 by Frederick Muriuki Muriithi, last updated on Apr 07 2022 by Zachary Sloan
...trait_id=1448231_at&dataset=HC_M2_0606_P
>
> jacs123
I (fredm) tried this out, and it seems there is still an issue here.
This appears to no longer be an issue; it was probably addressed along...
- 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`...
- 'TempDataSet' object has no attribute 'query_for_group' (error)
✓ issue opened on Mar 22 2022 by Frederick Muriuki Muriithi, last updated on Sep 28 2022 by Alexander_Kabui
...might also be interested in this issue
## Notes 28/9/22
this issue has not being reported for a while since jul 16,2021
The error is also not reproducible
closing down this until a new issue is raised
- 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...
- 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
...issue appears to be caused by marker namees being duplicated. If a marker name appears in an earlier chromosome, it ends up displayed first in the GEMMA results for a later chromosome.
For example...
- Global search does not close connections properly (and is slow)
✓ issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Oct 14 2022 by Arun Isaac
...of log file info.
In fact, every row in the table has a SQL query that does not close the connection properly.
## Resolution
The new xapian search does not use the SQL database at all. Therefore 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
...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 the global...
- correlation error: 'NoneType' object is not iterable
✓ issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Apr 13 2022 by Alexander Kabui
.../wqflask/wqflask/correlation/show_corr_results.py", line 473, in process_samples
for sample in sample_names:
```
## notes
codebase for gn2 correlation had a rewrite
and this is no longer an issue
- Capture state of phenotypes in a HASH
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
...API - so people van validate client side (as a feature).
This mentions RDF - which I think
* aruni
was involved in. I (fredm) have tagged them here, for their evaluation of the relevance of this issue...
- AI UI Enhancements
issue opened on Mar 01 2024 by Pjotr Prins; 0 of 3 tasks done
...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 it...
- Automatically find broken links on GN2
✓ issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Oct 12 2022 by Munyoki Kilyungi; 2 of 2 tasks done
...moved the new gn2 CI
### Resolution
This was added to Mechanical Rob here:
=> https://github.com/genenetwork/genenetwork2/pull/555
Making Mechanical Rob should it fail is an entirely different issue.
- 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...
- 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
...dumping RDF has already been done in:
=> https://github.com/genenetwork/dump-genenetwork-database dump-genenetwork-database
Also, vector/matrix data should be put in lmdb, and this is a separate issue...
- 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
...probably a permission issue.
## Files generated in /tmp (later)
Not unique file names appearing in TMPDIR:
```
-rw-r--r-- 1 gunicorn-genenetwork2 gunicorn-genenetwork2 337 Apr 2 07:03 175.png
-rw-r--...
- 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.