- 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...
- Designing an issue tracker on gemini
✓ issue opened on Jul 25 2021 by Pjotr Prins, last updated on Feb 02 2022 by Pjotr Prins
...critical bug
* enhancement
* in progress
* testing
* later
* documentation
* help wanted
* closed
the keyword statement may have aliases, such as tag and kanban. To undo a keyword simply remove them...
- 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
...progress
* keywords: tissue, edit issue
## Description
Add an `Edit Issue` link on each issue that drops the user in the forge's (currently GitHub) editting mode for the selected file.
For an example...
- 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...
- 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
...it
* [x] Submit patches for review
## Editing metadata
* [x] Research ways of editing that text if the user really wants to
* [x] Inspect how GN1 did the edits
* [x] Work out if the edits are feasible/...
- 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
...access by malicious users and bots.
The main endpoint to fetch and edit a file is:
```
genenetwork.org/editor/edit?file-path=<relative file path>
```
This loads the editor with the content for editing.
- 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
...alexm
* type: enhancement
* status: IN PROGRESS
* keywords: markdown,editor
## Tasks
* [x] implement markdown page editor
* [x] add live preview for page markdown on edit
* [] authentication(WIP)...
- Parsing genotyfiles
issue opened on Jul 11 2023 by Alexander_Kabui
...progress
## Once you identify 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/...
- 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
...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 first in the GEMMA results...
- 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
...in progress
* Keyword : 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...
- Capture state of phenotypes in a HASH
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
Capture state of phenotypes in a HASH
## Tags
* assigned: pjotrp, zsloan
* type: enhancement, feature-request
* status: in progress
* priority: medium
* keywords: phenotypes, REST, UI
## Description...
- 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
...does not match the observed issue.
## TODO
* [ ] Test in a similar environment to the CD environment to replicate the issue.
* [ ] Investigate the internals of the QTL library for any unintended `rm`...
- 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...
- Wrong CSV in ITP_10001 longevity dataset
✓ issue opened on Apr 11 2022 by BonfaceKilz, last updated on Apr 12 2022 by BonfaceKilz
...progress, metadata, phenotypes
## Description
[From Suheeta]:
"I downloaded the sample csv file for ITP_10001 to add a couple of attributes to it. What I see is that the csv file is somewhat messed up.
- Tux01 hard disk crash
issue opened on Sep 29 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...fortunately we have a BORG_BORG backup (a backup of the backup):
```
epysode:/export/backup$ borg extract --progress borg-borg::BORG_BORG_TUX01-Saturday-20210925-07:12:04
```
We are adding a new 4TB...
- 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
...(about an hour)
```
root@tux02:/export3/backup/tux01/borg# borg extract borg-tux01::borg-backup-mariadb-20211024-03:09-Sun --progress
```
Next move the dir to fast storage.
#### Symlink /var/lib/mysql...
- 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
...--progress /export2/backup/tux01/borg-tux01::borg-backup-mariadb-20220815-03:13-Mon
```
Extracting 430Gb takes about 90 minutes.
Now make sure mariadb is stopped. Copy the database to fast storage.
- Troubleshoot response inconsistencies for GN-llm
issue opened on Jan 10 2024 by Alexander_Kabui
...Progress
# Description
There are discrepancies when asking questions on Qnqa using Fahamu. Sometimes, responses take too long, and related queries with differing sentence structures may result in no...
- Search results presentation
issue opened on Apr 04 2023 by Alexander_Kabui
...in progress
* keywords: UI,search
## Notes
The idea is to research and find good design for search results in global search
Currently the results are displayed in tabular form and too many columns...
- 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
...progress
* keywords: UI, SNP, from github
## Description
=> https://github.com/genenetwork/genenetwork2/issues/395
### Description
After an update using the latest datatables from GUIX from
=> https...
- Report invalid search queries passed to the search API
issue opened on Feb 15 2023 by Arun Isaac, last updated on Apr 04 2023 by Alexander_Kabui
...progress
genenetwork2 offloads search to the genenetwork3 search API. When there is an error in the genenetwork3 API call, genenetwork2 has no idea what went wrong and cannot produce a good stacktrace.
- 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
...in progress
## Notes
having identified ways to link genofiles to Dataset
and fetching sample data and case attributes using them
we need to integrate the components intoa fully working module...
- 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
...in progress
* keywords: gn-auth, auth, redirect, login, completed, closed, done
* type: feature-request
## Description
The goal is to redirect users to the login page for services that require...
- 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
...progress
* kanban: pjotrp
* assigned: pjotrp, zachs, robw
## List of outstanding issues
(see also E-mail Rob 14 Sep 2021)
* [ ] Fix annotating metadata - or do we have GN2 alternative?
=> gn1-slowness...
- 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
...waiting on Danny to get back to me with the fix (which I'll then add to rqtl_wrapper.R)
## Tags
* type: bug
* assigned: zsloan, danny
* status: in progress, halted
* keywords: marker covariates...
- Add the option to save traits uploaded with the Submit Trait option
issue opened on Jul 19 2022 by Zachary Sloan
...-request
* status: open, in progress
* keywords: data, meta-data
# Description
Current the Submit Trait feature only allows for trait data (submitted as just a string of values) to be saved as a "temp"...
- 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
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
* keywords: guix-bioinformatics
* status: in progress...
- 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...
- Integrate styling of app with GN2
issue opened on Oct 28 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...in progress
* assigned: jgart
* type: bug
* priority: medium
* keywords: binderlite, notebooks, styling, UI
## Description
Currently using antiweb for styling with modifications.
=> https://git.sr.ht/~...
- Enable all DataTables to call the same code
issue opened on Jul 26 2022 by Zachary Sloan, last updated on Jul 27 2022 by Zachary Sloan
...progress
* keywords: tables, javascript
# Description
Currently most DataTables are drawn independently, so each separate page has its own DataTables initialization code. This results in inconsistency...
- Allow analyses to be done between traits from "individuals" groups and their corresponding "main" group
issue opened on Jul 21 2022 by Zachary Sloan
...open, in progress
* keywords: data, meta-data
# Description
Currently you can't do an analysis beween traits from the "main" BXD group and traits from any of the BXD individuals groups, but it should...
- Penguin2 RAID 5
issue opened 8 weeks ago by Pjotr Prins
...progress
# Description
The current RAID contains 3 disks:
```
root@penguin2:~# cat /proc/mdstat
md0 : active raid5 sdb1[1] sda1[0] sdg1[4]
/dev/md0 33T 27T 4.2T 87% /export
```
using /dev/...
- Annotation
issue opened on Sep 14 2022 by Pjotr Prins, last updated on Mar 14 2023 by Arun Isaac; 0 of 5 tasks done
...a matching reference genome. In the future we'll build this out with pangenome support.
# Tags
* assigned: pjotrp,zsloan,arthurc,robw
* priority: medium
* type: enhancement
* status: open, in progress...
- Add track for showing which regions in mouse/rat correspond to human regions to the mapping figure
issue opened on Jul 21 2022 by Zachary Sloan, last updated on Sep 14 2022 by Pjotr Prins
...in progress
* keywords: mapping
I currently have it displaying regions in mouse with text and a UCSC genome browser link to the corresponding human region as a track for the mapping figure.
# TODO
[X]...
- 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
...a guix shell/environment:
* bnw
* cronjob-gitea
* cronjob-pubmed (genecup)
* genecup
* gitea
* ipfs
* power
* rn6app
* singlecell
## Tags
* assigned: efraim, pjotrp
* type: bug
* status: in progress...
- Branding and front-end-services
issue opened on Jun 14 2023 by Pjotr Prins; 0 of 1 tasks done
...specific datasets
* + [ ] Show specific publications
* + [ ] Show specific twitter feed
# Tags
* assigned: pjotrp
* type: feature
* priority: high
* status: in progress
* keywords: website, branding
- Fix GN1 Network Graph
issue opened on Sep 15 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...Graph
* status: in progress
* kanban: pjotrp
* assigned: pjotrp, zachs
## Tracking
To reproduce this bug: select a 'shopping basket' and click on network graph. No image is shown.
We needed to revert...
- Linking genotype files to datasets
issue opened on Jul 07 2023 by Alexander_Kabui, last updated on Jul 11 2023 by Alexander_Kabui
...in progress
## Notes
A dataset can have multiple groups. In order to fetch all possible sample data fetch all possible groups in a dataset then use that to fetch all linked genofiles
As an example...
- 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
...fallback, deploy
* status: in progress
* priority: critical
# Tasks
* [X] 502 timeout errors
* [X] Rqtl2 not working
* [X] 413 error
* [ ] BNW error
* [ ] Monitor service - both systemd and sheepdog...
- 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
...progress
* priority: 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...
- 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
...progress
## Notes
since Genenetwork database does not have all genotype files when fetching sample data use genotypes to fetch trat data given a dataset and the trait
Having fetched the sample names...
- Apps
issue opened on Nov 19 2024 by Pjotr Prins, last updated 5 weeks ago by Pjotr Prins; 33 of 74 tasks done
...in progress
* priority: medium
* keywords: system, sheepdog, shepherd
# Tasks
* [ ] Get services running
* [ ] Move guix shell into containers
* [ ] Make sure the container starts up on reboot and/or...
- 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
...in progress
* keywords: slow query
# Tasks
* [ ] upgrade mariadb on production
* [ ] switch character type on ProbeSet table from latin1/utf8mb3 to utf8mb4 (and any other tables) - depends on mariadb...