- Variant Browser seems to be using mm9
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
Variant Browser seems to be using mm9
## Tags
* assigned:
* priority: unclear
* type: bug
* status: stalled
* keywords: variant browser, mm9, from github
## Members
* acenteno
* robw
* pjotrp...
- 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...
- 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
...a UCSC genome browser link to the corresponding human region as a track for the mapping figure.
# TODO
[X] Display track showing homology across mouse/human/maybe rat (done for mouse, won't be hard...
- 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
...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...
- Designing an issue tracker on gemini
✓ issue opened on Jul 25 2021 by Pjotr Prins, last updated on Feb 02 2022 by Pjotr Prins
...testing
* later
* documentation
* help wanted
* closed
the keyword statement may have aliases, such as tag and kanban. To undo a keyword simply remove them from the file.
Can't think of anything...
- 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
Report invalid search queries passed to the search API
* assigned: alex, arun
* tags: enhancement
* status: in progress
genenetwork2 offloads search to the genenetwork3 search API. When there is an...
- AI UI Enhancements
issue opened on Mar 01 2024 by Pjotr Prins; 0 of 3 tasks done
...until a first global search is done:
* [ ] When a global search is done, before the table show a line that people can use the text search:
```
------- [search]
GN searched for the term(s) "shh" in 754...
- Search results presentation
issue opened on Apr 04 2023 by Alexander_Kabui
Search results presentation
## Tags
* assigned: alex
* status:in progress
* keywords: UI,search
## Notes
The idea is to research and find good design for search results in global search
Currently...
- 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
...global search, db connections, medium priority, from github
## Description
=> https://github.com/genenetwork/genenetwork2/issues/418 From GitHub
Global search '*' causes loads of aborted connections...
- 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
...search results for GN2 look off.
Here's how it looked like in the past:
=> https://user-images.githubusercontent.com/11820306/82554424-8e0ac600-9b6e-11ea-9a50-f53506eb44a5.png Screen Shot 2020-05-20...
- 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
...Consortium M430v2 (Jun06) PDNN 1457545_at 9530036O11Rik long non-coding RNA, expressed sequence tag (EST) AK035474 with high bladder expression antisense EST 14 Kb upstream of Shh...
- 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
...Ember
```
Turns out that lily URLs were hard-coded in the source. So, that was an easy fix. There are still some complaints about CSS links missing in the browser console, but until someone sees...
- 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
...('brca2' IN BOOLEAN MODE)
```
With xapian search that is no longer done through SQL. We'll need to toy a bit with this index. We need to check what 'menu' search does, though we want to consolidate...
- 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
...question, which can override the defaults
Converted tables:
[X] - Search Results
[X] - Collection View
[X] - Collection List
[X] - Correlation Results
[X] - Global Search
[X] - Trait Page Sample Table...
- Penguin2 RAID 5
issue opened on Feb 28 2025 by Pjotr Prins
...then
search --no-floppy --fs-uuid --set=root --hint-bios=hd2,msdos1 --hint-efi=hd2,msdos1 --hint-baremetal=ahci2,msdos1 7ff268df-cb90-4cbc-9d76-7fd6677b4964
else
search...
- Annotation
issue opened on Sep 14 2022 by Pjotr Prins, last updated on Mar 14 2023 by Arun Isaac; 0 of 5 tasks done
.../do_search.py#L819-L857 - Search queries
notably the Position Search (the most "ambitious" version of this would allow for querying based off of different assemblies, but I can't think of a good way...
- Apps
issue opened on Nov 19 2024 by Pjotr Prins, last updated 5 weeks ago by Pjotr Prins; 33 of 74 tasks done
...on reboot (systemd)
* [-] singlecell (siamak)
* [-] rn6app (hao - remove)
* [-] genome-browser (defunct)
To fix them we need to validate the sheepdog monitor and make sure they are working in either...
- 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
...server. If you entered the URL manually please check your spelling and try again.
```
## Tasks
* [x] code to search for broken links in web pages
* [x] run gn2 on CI as a background task to search...
- 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
...publications are in GN related to addiction and published after 2010?
We want to make search easy and to disambiguate terms.
### Describe alternatives you've considered
Modelling everything in MariaDB.
- 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
...I created them outside a container
```
-rw-r--r-- 1 root root 10M Apr 2 07:03 4OJCzmGV.cross
-rw-r--r-- 1 root root 10M Apr 2 07:03 6cExgwkd.cross
```
# Purescript browser buttons not showing...
- Fetch trait names for phenotypes
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
..."Central nervous system, behavior, learning and memory: Morris water maze search-time preference, amount of time spent in the trained quadrant of the pool minus mean time in the alternative quadrants...
- Branding and front-end-services
issue opened on Jun 14 2023 by Pjotr Prins; 0 of 1 tasks done
...allow for rebranding and multiple servers of GN2 services. A community website can be created in this way with its own 'portal', dedicated search and interactive GN tooling.
To make it even more fun...