- 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...
- 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...
- 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
...global search query.
## Indices
ProbeSet has a large number of columns, indices and full text indices(!)
## Nailing it down
The obvious thing to try is to reduce the query and see what speeds it up...
- 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
Fix Broken Global Search UI
## Tags
* Assigned: alexm, zsloan
* Priority: high
* status: in progress
* Keyword : search, UI, bug, Refactor
* Type: UI, bug
## Description
The Global search UI layout...
- 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...
- 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...
- 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
...curl, try
```
curl -G https://query.wikidata.org/sparql -H "Accept: application/json; charset=utf-8" --data-urlencode query="SELECT DISTINCT * where {
wd:Q158695 wdt:P225 ?o .
} limit 5"
{
"head"...
- Variant Browser seems to be using mm9
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
...do not match the query.
Searching for a gene gives correct coordinates in the search box at http://www.genenetwork.org/snp_browser, but the results are for the same coordinates in mm9 (see screenshot).
- 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...
- Fetch trait names for phenotypes
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
.../564 From GitHub
The 'Fetch Trait Info' query returns detailed information for transcript expression traits, but not for traits from the 'Publish' database.
### Describe the solution you'd like
For...
- 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
...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 more to add to make it really useful...
- 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
...the global shepherd guix profile and loading guix-bioinformatics at service start time to start their services. This is bad because:
* we aren't using per-service guix-bioinformatics worktrees, so...
- Slow query
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
Slow query
## Tags
* assigned: Uditgulati
* priority: high
* status: stalled
* keywords: slow query, from github
## Description
=> https://github.com/genenetwork/genenetwork2/issues/419...
- 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...
- 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...
- 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...
- 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...
- 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
...showing homology across mouse/human/maybe rat (done for mouse, won't be hard to also enable for other species)
[ ] Make it display an arrow depending on the strand (whether the query strand matches...
- 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
...related genes?
* What 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...
- 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
...(est. 1-2 hours)
Set up a global Mariadb
```
guix package -i mariadb -p /usr/local/guix-profiles/mariadb
```
Usually I use the Debian version to set up defaults
```
apt-get install mariadb
cd /etc/...
- 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
...query for the trait:
```
PREFIX gn: <http://genenetwork.org/>
SELECT ?name ?dataset ?dataset_group ?title ?summary ?aboutTissue ?aboutPlatform ?aboutProcessing
WHERE {
?dataset gn:accessionId "GN112"...
- 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...
- 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
...path, query, fragment = parse_url(url)
File "/gnu/store/a39cgbdawj9vp24nsz9q25sf9g5vda7c-profile/lib/python3.10/site-packages/urllib3/util/url.py", line 397, in parse_url
return six.raise_from...