- Designing an issue tracker on gemini
✓ issue opened on Jul 25 2021 by Pjotr Prins, last updated on Feb 02 2022 by Pjotr Prins
...flexible, but common ones are
* request
* bug
* critical bug
* enhancement
* in progress
* testing
* later
* documentation
* help wanted
* closed
the keyword statement may have aliases, such as tag...
- 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...
- 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...
- Wrong CSV in ITP_10001 longevity dataset
✓ issue opened on Apr 11 2022 by BonfaceKilz, last updated on Apr 12 2022 by BonfaceKilz
...bug
* status: closed
* priority: critical
* keywords: critical bug, in progress, metadata, phenotypes
## Description
[From Suheeta]:
"I downloaded the sample csv file for ITP_10001 to add a couple...
- 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
...bug
* priority: critical
* keywords: GN1
* status: in progress
* kanban: pjotrp
* assigned: pjotrp, zachs, robw
## List of outstanding issues
(see also E-mail Rob 14 Sep 2021)
* [ ] Fix annotating...
- 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
Annotate traits page with metadata from RDF
* assigned: bonfacem
* priority: high
* status: in progress
* keywords: rdf, critical, metadata
Read the design-doc here:
=> /topics/add-metadata-to-trait-...
- 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
...critical
## Tasks
* [X] fix redis queue and sheepdog server
* [X] check backups on tux01
* [ ] drop tux02 backups off-site
* [ ] backup ratspub, r/shiny, bnw, covid19, hegp, pluto services
* [ ] /etc...
- 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
...type: bug
* assigned: pjotrp
* keywords: systems, fallback, deploy
* status: in progress
* priority: critical
# Tasks
* [X] 502 timeout errors
* [X] Rqtl2 not working
* [X] 413 error
* [ ] BNW error...
- 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
...looks weird
## Tags
* assigned: zsloan
* type: bug
* priority: medium
* status: in progress
* keywords: UI, SNP, from github
## Description
=> https://github.com/genenetwork/genenetwork2/issues/395...
- AI UI Enhancements
issue opened on Mar 01 2024 by Pjotr Prins; 0 of 3 tasks done
AI UI Enhancements
## Tags
* Assigned: alexm, shelbys
* Keywords: UI, GNQA
* Type: critical
* Status: In Progress
## Description
This issue addresses user feedback received during the testing phase...
- 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
...a bit small, but it shoud not be critical here. Though I found
BUFFER CACHING:
The InnoDB Buffer Pool caches data and index pages. MyISAM only caches index pages.
Just in this area alone, MyISAM does...
- Fix GN1 Network Graph
issue opened on Sep 15 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...pjotrp, zachs
## Tracking
To reproduce this bug: select a 'shopping basket' and click on network graph. No image is shown.
We needed to revert on
=> https://github.com/genenetwork/genenetwork1/commit/...
- 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
...Bug
* status: in progress
* keywords: external, qtl, rqtl, bug, logs
## Description
For QTL analysis, we invoke the `rqtl` script as an external process through Python's `subprocess` module.
For...
- 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
...zachs
* keywords: bug
* status: in progress
* priority: high
This issue appears to be caused by marker namees being duplicated. If a marker name appears in an earlier chromosome, it ends up displayed...
- 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
...-bioinformatics git server that is *not* gitlab or github.
I think we should move to ssh keys and cgit. The latter has to run in a container, ideally.
## Tags
* assigned: efraimf, pjotrp
* type: bug...
- Integrate styling of app with GN2
issue opened on Oct 28 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...bug
* priority: medium
* keywords: binderlite, notebooks, styling, UI
## Description
Currently using antiweb for styling with modifications.
=> https://git.sr.ht/~sircmpwn/antiweb antiweb
Copying nav...
- Capture state of phenotypes in a HASH
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
...//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 we should create these for phenotype...
- 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
...search, UI, bug, Refactor
* Type: UI, bug
## Description
The Global search UI layout is broken on certain browser versions.
This issue was reported to occur for **Firefox Version 128.3.1** ESR...
- 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...
- Apps
issue opened on Nov 19 2024 by Pjotr Prins, last updated 5 weeks ago 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/...
- 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...
- Marker covariates implemented wrong in rqtl_wrapper.R
issue opened on Sep 22 2021 by Zachary Sloan, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...in rqtl_wrapper.R is wrong. For the time being,
I've removed this option. Currently just waiting on Danny to get back to me with the fix (which I'll then add to rqtl_wrapper.R)
## Tags
* type: bug...
- Return canned text if notebook description returns none
issue opened on Oct 28 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
Return canned text if notebook description returns none
## Tags
* type: bug
* assigned: jgart
* priority: high
* status: in progress
* keywords: binderlite, notebooks
## Description
Notebooks that do...
- Gn Markdown Editor implementation
issue opened on Aug 07 2023 by Alexander_Kabui, last updated on Sep 11 2023 by Alexander_Kabui; 4 of 5 tasks done
...preview for page markdown on edit
* [] authentication(WIP)
* [x] commit changes to github repo
* [x] UI improvement
## Notes
for quick server setup refer to the documentation below:
=> https://github...
- Annotation
issue opened on Sep 14 2022 by Pjotr Prins, last updated on Mar 14 2023 by Arun Isaac; 0 of 5 tasks done
.../End)
=> https://github.com/genenetwork/genenetwork2/blob/df36cc808e21202075d32559c9f295087bd8aee2/wqflask/base/trait.py#L528-L597
where max LRS locus position is fetched for traits
=> https://github...
- 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
It is
used to fire up a guix shell/environment:
* bnw
* cronjob-gitea
* cronjob-pubmed (genecup)
* genecup
* gitea
* ipfs
* power
* rn6app
* singlecell
## Tags
* assigned: efraim, pjotrp
* type: bug...
- rewrite sampledata fetching with genofiles using scheme
issue opened on Jul 19 2023 by Alexander_Kabui, last updated on Jul 26 2023 by Alexander_Kabui; 2 of 6 tasks done
...intoa fully working module
This is in turn be used to dump data to lmdb
We chose scheme to accomplish the task
See code:
=> https://github.com/BonfaceKilz/gn-data-vault.git
=> https://github.com/...
- 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...
- Allow analyses to be done between traits from "individuals" groups and their corresponding "main" group
issue opened on Jul 21 2022 by Zachary Sloan
...as a decorator function) that, prior to an analysis, checks if there are traits from both a "main" and "individuals" group (for example a BXDPublish phenotype and a phenotype from BXD-LongevityPublish).
- 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
...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.com/genenetwork/genenetwork2/pull/875
- 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/...
- Tux02 Production
issue opened on Oct 07 2021 by Pjotr Prins, last updated on Dec 14 2022 by Pjotr Prins; 17 of 22 tasks done
...longer get 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)...
- 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...