- Designing an issue tracker on gemini
✓ issue opened on Jul 25 2021 by Pjotr Prins, last updated on Feb 02 2022 by Pjotr Prins
...blame to figure out who did what.
## Closing issues
Moving an issue file will disconnect the git record. Therefore simple add
* closed
## Converting github issues
### Converting issues from a github...
- GN1 github problem
issue opened on Dec 17 2022 by Pjotr Prins
...github problem
When trying to push to github, a commit from 2018 is blocking:
```
tux01:~/genenetwork1$ git push
Enumerating objects: 41, done.
Counting objects: 100% (41/41), done.
Delta compression...
- Sheepdog
issue opened on Nov 08 2021 by Pjotr Prins, last updated on Jul 01 2022 by Arun Isaac; 3 of 17 tasks done
...exists)
* [ ] synchronize between queues using a dump
* [ ] sheepdog_expect.rb - expect PINGs
* [ ] sheepdog_rsync.rb - test for 'total size is 0'
* [ ] sheepdog_list tag and filter switches improve...
- 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
...Pre-transfer: 0.000551s
Start transfer: 24.792926s
Total time: 24.793015s
```
That rules out container and nginx streaming issues.
So the problem is with GN and its DBs. The gn-machines is used from...
- csv export meta data are not commented out
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
...out
## Tags
* assigned: zsloan
* priority: high
* type: bug
* status: unclear
* keywords: CSV, from github, meta data
## Description
=> https://github.com/genenetwork/genenetwork2/issues/594 From...
- 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
...steps
* [x] Spec out LMDB integration and how it would work out with current statistical operations. Collaborate with Alex/Fred on this
## Resolution
This has been worked on in
=> https://github.com/...
- 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
...annotation, from github
## Tasks
* [ ] Fix PHP view
* [ ] Fix CKEDITOR
## Description
Turns out that it is a PHP page that is not working. Also CKEDITOR is not visible.
=> https://github.com/...
- Wrong CSV in ITP_10001 longevity dataset
✓ issue opened on Apr 11 2022 by BonfaceKilz, last updated on Apr 12 2022 by BonfaceKilz
...being stripped out. As a consequence, opening the csv file in Excel (or similar) software resulted in data that seems jumbled up.
### Tue 12 Apr 2022 13:33:31 EAT
The relevant fixes:
=> https://github...
- 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
...an ontology exists and it looks sensible we should reuse that. If non-existent, we create our own ontology. Obviously we can't get away from adding free flow textual fields. What we want to lift out...
- BXD102xBXD077F1 Error
✓ issue opened on Mar 22 2022 by Frederick Muriuki Muriithi, last updated on Apr 07 2022 by Zachary Sloan
...from github, closed
## Description
=> https://github.com/genenetwork/genenetwork2/issues/612 From GitHub
> Hi,
>
> There is an error when I click on Compute in Calculate Correlations. It does not...
- 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...
- 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
...proxy also needs to run.
```
su gn2
cd ~/gn3_production
git clone https://github.com/genenetwork/gn-proxy.git
```
See README
### Trouble shooting
Check the server log for errors from the server. There...
- Fix GN1 Network Graph
issue opened on Sep 15 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...//
github.com/genenetwork/genenetwork1/commit/88a6cb549cc318a961325666aed06f3196a5475d Commenting
out functionality
Reverting on that code still won't show the image contained in
```
<img border="0"...
- 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...
- 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
...UI, SNP, from github
## Description
=> https://github.com/genenetwork/genenetwork2/issues/395
### Description
After an update using the latest datatables from GUIX from
=> https://github.com/...
- Slow query
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
...from github
## Description
=> https://github.com/genenetwork/genenetwork2/issues/419 From GitHub
These queries take 3 minutes and are pretty insane!
```
Query_time: 187.220555 Lock_time: 0.075028...
- Multi-trait heat map failed
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
...from github
## Members
* zsloan
* pjotrp
* echesler
## Description
=> https://github.com/genenetwork/genenetwork2/issues/368 From GitHub
Selected multiple traits from phenotype correlations to Ap3m2...
- Fetch trait names for phenotypes
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
...phenotype, from github
## Members
* robw
* rupertoverall
## Description
=> https://github.com/genenetwork/genenetwork2/issues/564 From GitHub
The 'Fetch Trait Info' query returns detailed information...
- Unable to open new tab for mapping/ correlations with Chrome
✓ issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Apr 18 2023 by Munyoki Kilyungi
...chrome, UI, from github
## Description
=> https://github.com/genenetwork/genenetwork2/issues/399 From GitHub
Based off
=> https://github.com/genenetwork/genenetwork2/pull/394 Pull Request #394.
I'd...
- 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
...GN1, GN2, broken links, from github
## Members
* Millak
* pjotrp
* zsloan
* alex
* bonfacem
* robw
## Description
=> https://github.com/genenetwork/genenetwork2/issues/420 From GitHub
@Millak found...
- Adding principal component to collection returns an error
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Apr 07 2022 by Alexander Kabui
...collections, from github
## Members
* rupertoverall
## Description
=> https://github.com/genenetwork/genenetwork2/issues/559 From GitHub
### Describe the bug
When calcuating principal components from...
- Variant Browser seems to be using mm9
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
...stalled
* keywords: variant browser, mm9, from github
## Members
* acenteno
* robw
* pjotrp
## Description
=> https://github.com/genenetwork/genenetwork2/issues/581 From GitHub
When looking for SNPs...
- GN1 annotation page broken
issue opened on Dec 23 2022 by Pjotr Prins
...from github
## Description
=> https://github.com/genenetwork/genenetwork2/issues/421 From GitHub
=> http://gn1.genenetwork.org/webqtl/main.py?FormID=annotation The annotations page in GN1
is broken.
- 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
...priority, from github
## Description
=> https://github.com/genenetwork/genenetwork2/issues/418 From GitHub
Global search '*' causes loads of aborted connections... I mean
```
2020-08-15 2:53:58...
- 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
...from github, high priority
## Description
=> https://github.com/genenetwork/genenetwork2/issues/374 From GitHub
Dear Developer,
When calculating correlation:
(GeneNetwork error: 'NoneType' object...
- Error when attempt to zoom to a chromosome after mapping a PCA trait
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
...from github, high priority
## Description
=> https://github.com/genenetwork/genenetwork2/issues/367 From GitHub
When I produced a PCA trait in GN2, I could map fine, but when I selected a particular...
- '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
...from github
## Description
=> https://github.com/genenetwork/genenetwork2/issues/592 From GitHub
After successful entry of new BXD trait data (both my own data and the example BXD set from...
- 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
...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 in...
- Capture state of phenotypes in a HASH
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
...REST, UI
## Description
=> https://github.com/genenetwork/genenetwork2/issues/551 From GitHub
To represent the state of the database we need to start using HASH values or UUIDs. For phenotypes...
- 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...
- Apps
issue opened on Nov 19 2024 by Pjotr Prins, last updated on Oct 09 2025 by Pjotr Prins; 33 of 74 tasks done
...//github.com/satijalab/seurat/issues/8804
The 4 year old code lives at
=> https://github.com/genenetwork/singleCellRshiny
and it looks like lines like these need to be updated:
=> https://github.com/...
- 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
...Recently epysode was reinstated after hardware failure. I took the opportunity to reinstall the machine. The backups are described in the repo (genenetwork org members have access)
=> https://github...
- 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
...case from auth)
* `email` (identifier email from the user, in our case from auth)
* `commit_message`
If the request succeeds, the response should be:
```json
{
"status": "201",
"message": "Committed...
- Fetch trait data using genofiles
issue opened on Jul 11 2023 by Alexander_Kabui, last updated on Jul 13 2023 by Alexander_Kabui; 2 of 3 tasks done
...FROM
(SELECT DISTINCT st.Name as 'Sample', ifnull(pd.value, 'x') as 'Value',
ifnull(ps.error, 'x') as 'SE', ifnull(ns.count, 'x') as 'Count', ps.StrainId as 'StrainId'
FROM PublishFreeze pf JOIN...
- Linking genotype files to datasets
issue opened on Jul 07 2023 by Alexander_Kabui, last updated on Jul 11 2023 by Alexander_Kabui
...Families(BXD family, B6D2RI, B6D2F2) -> Genofiles related to this (BXD.geno, B6D2RI.geno, B6D2F2.geno)
* How to fetch Families given a species
```sql
SELECT InbredSet.Name, InbredSet.FullName
FROM...
- 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...
- 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
...Redirect users to the login page if they are not logged in.
* [x] Implement a redirect to the correct resource after users log in.
## Notes
See this PR for commits that fixes this:
=> https://github...
- Using guix-bioinformatics in a channels.scm file
issue opened on Aug 15 2021 by Efraim Flashner, last updated on Oct 09 2022 by Pjotr Prins
...a channels.scm file
channels.scm works fine. Only problem is that we don't have a guix-bioinformatics git server that is *not* gitlab or github.
I think we should move to ssh keys and cgit. The latter...
- 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
...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/genenetwork/gn-gemtext-threads/...
- Allow analyses to be done between traits from "individuals" groups and their corresponding "main" group
issue opened on Jul 21 2022 by Zachary Sloan
...do an analysis beween traits from the "main" BXD group and traits from any of the BXD individuals groups, but it should technically be possible to do so as long as there's a mapping of individuals...
- 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
...copied. We only restore from backup. First because these are reproducible [installs]. Second because the backup should be in a sane state(!).
Restoring a database from backup (about an hour)
```
root@...
- 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
...logs
## Description
For QTL analysis, we invoke the `rqtl` script as an external process through Python's `subprocess` module.
For reference, see the `rqtl_wrapper.R` script:
=> https://github...
- Branding and front-end-services
issue opened on Jun 14 2023 by Pjotr Prins; 0 of 1 tasks done
...generalised with a 'src=default' or 'src=portal-gn4msk' flag - or similar.
Based on this we can split the templates into reading specific headers/footers and feed those from other endpoints. Flask is...
- 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 from...
- 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
Zoomed mapping result are empty for certain traits
From RWW: For the following trait, if you zoom into a range for a specific Chromosome by clicking the top pink bar ("8x expanded WebQTL map") no...
- Integrate styling of app with GN2
issue opened on Oct 28 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...notebooks, styling, UI
## Description
Currently using antiweb for styling with modifications.
=> https://git.sr.ht/~sircmpwn/antiweb antiweb
Copying nav bar and fonts from GN2 will make the app look...