- Fix GN1 Network Graph
issue opened on Sep 15 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
Fix GN1 Network Graph
Status: the network graph works on production. PDF output is empty, however.
## Tags
* type: bug
* priority: high
* keywords: GN1, Network Graph
* status: in progress
* kanban...
- 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 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
...fairly trivial. Next to a pangenome, which is a graph on DNA,
we should present metadata in a structured way (a graph on everything
else).
Metadata and pangenomes ought to go hand in hand
### Describe...
- 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
...GN2 the complexity has increased a lot because of interacting services and a larger dependency graph.
Here I track what it takes today to install a fallback instance of GN2 that is 'frozen' in time.
- 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
...3.741e-05 32.09 4.585 socket.py:938(getaddrinfo)
```
* The above is consistent all the analysis I've done across all the profile dumps.
* Testing my theory out:
```
@app.route("/test-network")...
- Apps
issue opened on Nov 19 2024 by Pjotr Prins, last updated 12 days ago by Pjotr Prins; 33 of 74 tasks done
.../logs/bnw-server=/var/log --network
ln -s /gnu/store/0hnfb9ynnxsig3yyprwxmg5h6c9g8mry-run-container /usr/local/bin/bnw-app-container
```
systemd service:
```
root@tux02:/etc/systemd/system# cat bnw-app-...
- 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
...-1.3.0-9.f743f20
* [X] set up nginx (Debian)
* [X] test ipmi console
* [X] test ports (nginx)
* [?] set up network for external tux02
* [X] set up deployment evironment
* [X] sheepdog copy database...
- csv export meta data are not commented out
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
...py?FormID=sharinginfo&InfoPageName=BXDPublish
Name,Value,SE,N
BXD1,3125.333,803.776,6
BXD2,540.167,448.724,6
```
The metadata need to be commented out and the empty line needs to be removed. R expects...
- 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
...out if the edits are feasible/important to work on and communicate to PJ/Arun
## Next steps
* [x] Spec out LMDB integration and how it would work out with current statistical operations. Collaborate...
- Annotation
issue opened on Sep 14 2022 by Pjotr Prins, last updated on Mar 14 2023 by Arun Isaac; 0 of 5 tasks done
...out with pangenome support.
# Tags
* assigned: pjotrp,zsloan,arthurc,robw
* priority: medium
* type: enhancement
* status: open, in progress
* keywords: mapping, architecture
# TODO
* [ ] Point out...
- Wrong CSV in ITP_10001 longevity dataset
✓ issue opened on Apr 11 2022 by BonfaceKilz, last updated on Apr 12 2022 by BonfaceKilz
...be stripped out. Here's a current snip of how that looks like:
```
JL00005,896.000000,x,x,896,4/22/04,,4OHPBN_J,Oct,,0^M,M,JL,1,2004
JL00006,1077.000000,x,x,1077,4/22/04,,4OHPBN_J,Apr,,0^M,M,JL,1,2004...
- GN1 annotation page broken
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Dec 17 2022 by Pjotr Prins; 0 of 2 tasks done
...5.1.6 (cli) (built: Mar 18 2014 20:48:55)
Copyright (c) 1997-2006 The PHP Group
Zend Engine v2.1.0, Copyright (c) 1998-2006 Zend Technologies
In guix-bioinformatics we have
```
php 5.6.40 out...
- Designing an issue tracker on gemini
✓ issue opened on Jul 25 2021 by Pjotr Prins, last updated on Feb 02 2022 by Pjotr Prins
...file. Though, unlike other issue trackers, this is not obligatory. One can insert notes using the '>' prefix
> This is a comment
Or one can simply use git blame to figure out who did what.
## Closing...
- 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...
- Penguin2 RAID 5
issue opened on Feb 28 2025 by Pjotr Prins
.../sdd1 393G 121G 252G 33% /
# swap
/dev/sdd5 partition 976M 76.5M -2
```
We can therefore add four new disks in slots /dev/sdc,sde,sdf,sdh
penguin2 has no out-of-band and no serial connector...
- 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
...AND ProbeSetFreeze.public > 0 ORDER BY species_name, inbredset_name, tissue_name, probesetfreeze_name, probeset_name LIMIT 600;
```
To find out what index is problematic we first look at sizes. Tables...
- 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
...(source_url), None)
File "<string>", line 3, in raise_from
urllib3.exceptions.LocationParseError: Failed to parse: http://localhost:8893api/rqtl/compute
```
The error points out a missing slash...