- 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...
- 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_borg
* [ ] check whether rsync dir exists, repo valid and/or no lock before proceeding
* [ ] send digest E-mails
* [ ] smart state E-mails on services going down
* [ ] block on root user if...
- 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...
- 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
...-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 of log file info.
In fact, every row...
- 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.
- 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
...ipmi console
* [X] test ports (nginx)
* [?] set up network for external tux02
* [X] set up deployment evironment
* [X] sheepdog copy database backup from tux01 on a daily basis using ibackup user
* [X]...
- 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...
- 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 on Oct 09 2025 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...
- 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
...(hedgehog) mid distal 3' UTR 5 28.457155 9.279090909090911 12.7711275309832 rs8253327 0.306 -0.214087568058076 1 191.908118
real 0m0.010s
user...