- 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
...aborted connections... I mean
```
2020-08-15 2:53:58 140273206434560 [Warning] Aborted connection 45219 to db: 'db_webqtl' user: 'webqtlout' host: '127.0.0.1' (CLOSE_CONNECTION)
```
generating 6Mb...
- 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...
- Designing an issue tracker on gemini
✓ issue opened on Jul 25 2021 by Pjotr Prins, last updated on Feb 02 2022 by Pjotr Prins
...testing
* later
* documentation
* help wanted
* closed
the keyword statement may have aliases, such as tag and kanban. To undo a keyword simply remove them from the file.
Can't think of anything...
- CD is slow
issue opened on Jul 20 2025 by Pjotr Prins, last updated on Jul 24 2025 by Pjotr Prins; 2 of 8 tasks done
...Consortium M430v2 (Jun06) PDNN 1457545_at 9530036O11Rik long non-coding RNA, expressed sequence tag (EST) AK035474 with high bladder expression antisense EST 14 Kb upstream of Shh...
- Tux02 Production
issue opened on Oct 07 2021 by Pjotr Prins, last updated on Jun 13 2025 by Pjotr Prins; 17 of 22 tasks done
...the recovered backup. Restart the DB and run mysql_upgrade followed by our tests. E.g.
```
systemctl stop mariadb
ln -s /export2/mysql/borg-backup-mariadb-20211024-03\:09-Sun /var/lib/mysql
systemctl...
- Parsing genotyfiles
issue opened on Jul 11 2023 by Alexander_Kabui
...the genofile 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...
- Add the option to save traits uploaded with the Submit Trait option
issue opened on Jul 19 2022 by Zachary Sloan
...limited period of time).
There are two main changes/additions that should be made to this:
- Allow data to be submitted via a CSV upload
- Allow data to be saved to the DB via an "Add" (or maybe "Save")...
- csv export meta data are not commented out
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
...45-60 min after injection in an activity chamber for males [n beam breaks]"
"Authors: Philip VM, Ansah TA, Blaha CD, Cook MN, Hamre KM, Lariviere WR, Matthews DB, Mittleman G, Goldowitz D, Chesler EJ"...
- 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
.../lib/mysql
```
Check them and symlink the DB dir:
```
root@epysode:/export/tux01-mirror#
cp -vau /export2/tux01-restore/home/backup/tux01_mariadb_new .
systemctl stop mariadb
ln -s /export/tux01-mirror/...
- 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 presentation
issue opened on Apr 04 2023 by Alexander_Kabui
...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/genome/?term...
- 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...
- 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
...pink bar ("8x expanded WebQTL 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...
- AI UI Enhancements
issue opened on Mar 01 2024 by Pjotr Prins; 0 of 3 tasks done
...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 otherwise anyhow...
- Variant Browser seems to be using mm9
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
...in mm9 (see screenshot).
The example is for a search for 'Snx6' (chr12 54.746356 - 54.795662).
=> https://user-images.githubusercontent.com/35666678/119680694-b6906480-be41-11eb-9070-9f4c2dffb499.png...
- 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/...
- 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...
- Wrong CSV in ITP_10001 longevity dataset
✓ issue opened on Apr 11 2022 by BonfaceKilz, last updated on Apr 12 2022 by BonfaceKilz
...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 CSV file is technically fine.
- 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
...-20210829-04:20-Sun
real 17m32.498s
user 8m49.877s
sys 4m25.934s
```
This all contrasts heavily with restoring 300GB from Amazon S3.
Next restore the GN2 home dir
```
root@epysode:/# borg...
- 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
...user really wants to
* [x] Inspect how GN1 did the edits
* [x] Work out if the edits are feasible/important to work on and communicate to PJ/Arun
## Next steps
* [x] Spec out LMDB integration and how...
- Apps
issue opened on Nov 19 2024 by Pjotr Prins, last updated 3 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...