- Redesign Global Search Design
✓ issue opened on Sep 26 2024 by Alexander_Kabui, last updated on Oct 16 2024 by Alexander_Kabui; 2 of 2 tasks done
...model the global search on the NCBI PubMed interface. We should remove the `?` button, which seems to be confusing for users, and have a better user guide.
## Tasks
* [x] Redesign the global search...
- Cleanup GN2 Base HTML File
✓ issue opened on Sep 23 2024 by Alexander_Kabui, last updated on Oct 16 2024 by Alexander_Kabui; 3 of 3 tasks done
.../genenetwork2/pull/877
## Notes 26/09/2024
It was agreed that global search should be a feature for all pages,
As such all files need to inherit from the global search which
defines the global search.
- Global search problems
✓ issue opened on Aug 26 2022 by Pjotr Prins, last updated on Oct 14 2022 by Arun Isaac; 1 of 2 tasks done
Global search problems
Global search is the top bar of GN2.
Note we are replacing search with xapian. So this is less important.
## Tags
* assigned: pjotrp, zsloan
* status: later
* priority: low...
- Global Search Performance/Optimisation
issue opened 30 hours ago by Munyoki Kilyungi; 0 of 3 tasks done
Global Search Performance/Optimisation
* assigned: bonfacem, pjotrp
* status: in-progress
## Description
Global search is slow. Search latency sits at ~30 seconds. Historically, identical queries...
- 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...
- 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...
- Enter key in global search field
✓ issue opened on Feb 13 2023 by Arun Isaac, last updated on Apr 04 2023 by Alexander_Kabui
...in global search field
## Tags
* assigned: alex
* status: completed, closed
* keywords: search,UI
## Notes
In the home page, putting in a search query in the global search field and pressing the Enter...
- 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: Unhandled Error
✓ issue opened on Mar 04 2024 by Frederick Muriuki Muriithi, last updated on Sep 16 2024 by Frederick Muriuki Muriithi
Global Search: Unhandled Error
## Tags
* assigned: aruni, fredm
* priority: high
* type: bug
* status: closed
* keywords: global search, gn2, genenetwork2
## Description
=> https://github.com/...
- GNQA Integration to Global Search Design Proposal
✓ issue opened on Sep 02 2024 by Alexander_Kabui, last updated on Oct 16 2024 by Alexander_Kabui; 9 of 9 tasks done
...document outlines the design proposal for integrating GNQA into the Global Search feature.
## High-Level Design
### UI Design
When the GN2 Global Search page loads:
1. A request is initiated via HTMX...
- Global search doesn't seem to return phenotype traits
✓ issue opened on Nov 11 2022 by Zachary Sloan, last updated on Mar 14 2023 by Zachary Sloan
Global search doesn't seem to return phenotype traits
## Tags
* priority: high
* type: bug
* assigned: zsloan, aruni
* status: closed
* keywords: global search, phenotypes
## Description
For a search...
- Broken Aliases
issue opened on Oct 21 2024 by Frederick Muriuki Muriithi, last updated on Aug 15 2025 by Frederick Muriuki Muriithi; 3 of 4 tasks done
...1431728_at%0D%0A&search_terms_and=&accession_id=None&FormID=searchResult
in standard search.
But neither 1431728_at or '2310010I16Rik' has a hit in *global* search and the result for Ssh should...
- Add search syntax hints to web UI
✓ issue opened on Feb 15 2023 by Arun Isaac, last updated on Apr 04 2023 by Alexander_Kabui
...UI
The web UI of the global search should hint at the supported search syntax. For example, see how mumi (the Guix issue tracker) hints at the search query syntax when you click on the "Hint" dropdown.
- 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
...`alias`,`GenbankId`,`UniGeneId`,`Probe_Target_Description`),
```
BLOB and TEXT columns also can be indexed, but a prefix length must be given not to exceed the maximum length. In global search...
- Search results presentation
issue opened on Apr 04 2023 by Alexander_Kabui
...global search
Currently the results are displayed in tabular form and too many columns are presented to user overlapping the page
Design should be simple and eye catching to user
links to suggesetd...
- Implement No-Login Requirement for GNQA
✓ issue opened on Jun 04 2025 by Alexander_Kabui, last updated on Sep 01 2025 by Alexander_Kabui; 4 of 4 tasks done
...zero penalty
* [x] Add caching lifetime to save on token usage
* [x] Routes: check for referrer headers — if the previous search was not from the homepage, perform AI search
* [x] If global search...
- Xapian search queries
document created on Feb 13 2023 by Arun Isaac, last updated on Dec 03 2023 by Pjotr Prins
...global search").
General xapian search query syntax is documented on the xapian website.
=> https://getting-started-with-xapian.readthedocs.io/en/latest/concepts/search/queryparser.html
The specifics...
- 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...
- ProbeSetXRef
issue opened on Dec 29 2021 by Pjotr Prins, last updated on Jul 01 2022 by Arun Isaac
...led to a massive speed increase for typical ProbeSetXRef queries. Global search for brca2 went down from 13s to 4s! Try
=> http://genenetwork.org/gsearch?type=gene&terms=brca2
Not only global search...
- Xapian search
document created on May 02 2023 by Arun Isaac, last updated on Dec 03 2023 by Pjotr Prins
...main search engine (sometimes called the "global search" for historical reasons) is powered by Xapian, the excellent lightweight search engine library. This document aims to describe the architecture...
- Rework Fetching Settings
✓ issue opened on Sep 25 2022 by Munyoki Kilyungi, last updated on Oct 11 2023 by Munyoki Kilyungi
...make things less complex, and we get rid of many "asserts". This will force us to deal with missing values more gracefully; and as an example with how we handle missing values in global search using...
- Long samplenames overflow in Haplotype Analyst
issue opened on Nov 11 2022 by Zachary Sloan
...global search, phenotypes
## Description
For any BXD mapping, when Haplotype Analyst is selected, some of the more recently added samples have very long names that don't fit in the table
I guess...
- Add mouse data-set
issue opened on Jun 30 2022 by BonfaceKilz, last updated on Apr 18 2023 by Munyoki Kilyungi; 0 of 4 tasks done
...few other random traits mixed in; I first just searched for "Schughart"
in the global search) -
https://genenetwork.org/gsearch?type=phenotype&terms=H1N1
You're correct about there not being a (good)...
- Update production checklist
document created on May 10 2025 by Pjotr Prins, last updated on Sep 13 2025 by Pjotr Prins
...Last migration round is the move to tux03 (Sept2025)!
# Tasks
* [X] Install underlying Debian
* [X] Get guix going
* [X] Check database settings
* [X] Check gemma working
* [X] Check global search...
- Automated Testing
document created on Oct 12 2022 by Munyoki Kilyungi, last updated on Dec 03 2023 by Pjotr Prins
...cover the GN2/GN3 ones.
For GN2 we should write scripts that test:
* [ ] main menu selector
* [ ] search
* [ ] global search
* [ ] search with wild cards
* [ ] select items and add to shopping basket/...
- Automated Testing
✓ issue opened on Feb 10 2022 by Frederick Muriuki Muriithi, last updated on Oct 12 2022 by Munyoki Kilyungi; 0 of 10 tasks done
...cover the GN2/GN3 ones.
For GN2 we should write scripts that test:
* [ ] main menu selector
* [ ] search
* [ ] global search
* [ ] search with wild cards
* [ ] select items and add to shopping basket/...
- Set-up Virtuoso+Xapian on Production
✓ issue opened on Nov 22 2023 by Munyoki Kilyungi, last updated on Oct 28 2024 by Frederick Muriuki Muriithi; 1 of 1 tasks done
...unblock:
* Global Search in Production
=> https://github.com/genenetwork/genenetwork3/pull/137 Update RDF endpoints
=> https://github.com/genenetwork/genenetwork2/pull/808 UI/RDF frontend
## HOWTO...
- Meeting Notes
document created on Jun 11 2024 by John Nduli, last updated on Jan 10 2025 by Munyoki Kilyungi
...QNQA Search to global search.
* @shelby handling edits with the current open paper
Nice To Have:
* DEPRIORITIZED: @felix figure out how to fix large data uploads ie. most data sets are large e.g. 45GB.