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# Tasks for Alex
## Description
These are the tasks and issues to be handled by Alex.
Here are all open issues
=> https://issues.genenetwork.org/search?query=is%3Aopen+AND+assigned%3Aalexm&type=all
The search used for the list above is
> is:open AND assigned:alexm
You can refine the search by constraining the checks some more, e.g. to get high-priority issues
> is:open AND assigned:alexm AND priority:high
# Tasks
## This week
* [ ] Start application - Pwani
* - [X] Got all transcripts
* [+] Correlations - Fred is having issues - Rust updated on Guix
* - also take a look at long running SQL statement and large LIMIT value (check prod!)
* [ ] Friend of UTHSC - Pjotr needs to send forms
* [+] Disable spinner on production (check prod!)
* [+] Rqtl2 - BXD output work on CD
* - [ ] should go to production w. fredm
Disable for Production
* - [X] DO mice family file - children are heterozygous - family file contains parents->child
* - [X] DO GN2 compatible by generating .geno files
Test on CD
* [+ ] Minor refactorings - Rqtl2 is hacky
* [ ] Work in development system container and document
=> https://git.genenetwork.org/gn-machines/commit/?h=gn-local-development-container&id=589dcf32be90f5ec827cb6976d3cb5838d500ac0
* [+] Create terminal output for external processes on *PRODUCTION* (Rqtl1, Rqtl2, GEMMA, pair-scan are done --- WGCNA as a pilot, with @bonfacem and @pjotrp)
## (14/4/25)
* [x] Debug DO results for for genenetwork2
* [x] inspect results from gn3 and display mapping results
* [x] Debug db tunneling connection
* [x] Debug rendering huge datatables
## (21/4/25)
* [x] QTL computation for the DO dataset
* [x] Debug rendering large datasets using datatables
* [x] fix issue with qtl2 plot for DO dataset
* [x] Caching for qtl2 computations
* [] Pwani Campus Application
## 28/4/25
* [x] Push changes to CD/Production
* [x] Enable RQTL2 only for DO/bxd dataset
* [] look at integrating QTL for HS dataset
* [x] setup local container with bons
## 5/05/25
* [] Integrate hsrat dataset for rqtl2 mapping.
* [] Pwani campus application.
* [] Look at caching for genotype probabilities (rqtl2).
* [] Add full logs on the mapping results page.
* [x] Add test feature flag for rqtl2.
## 2/06/2025
* work onsubset for hs dataset;; define founder genotype files??
* script to dump genotypes to db with bons
* experiment with caching for Genotypic probabilities rds objects
* work on genenetwork llms how to make search without login
* masters ; submit documents
## 9/06/2025
* [x] no login for gnqna
* [-] hsrat rqtl2 integration: follow up on the dumping genotypes files to lmdb
## 16/06/2025
* [x] implementation for no login for gnqa users.
see issue here: https://issues.genenetwork.org/issues/gnqa/implement-no-login-requirement-for-gnqa
* [-] hsrat rqtl2 integration: follow up on the dumping genotypes files to lmdb with bons
* [] create rqtl2 adapter for reading cross from lmdb
## 23/06/2025
* [-] focus on documentation/source code for read cross ;;add option for reading lmdb
* [-] looking at thor an lmdb interface
* [x] implementation of no login for gnqna users ;; TODO push this code to cd.
* [x] for nologin llm provide the correct feedbacks to user if ai search does not meet criteria;; currently only static response `Please login to view AI generated summary`
## 30/06/2025
* [] rqtl2 lmdb interfac
e
7/7/2025
* [x] guix packaging for thor package
* [] reading metadata from lmdb file using thor
* [] working on reconstructing the genotype files to geno, geno_map and pheno_map file
* [] rate limiting for gnqna users.
* [] check on tokens for no logged in users
## Next week(s)
* [ ] Accelerate Xapian functionality - needs Aider key from Pjotr
* Check and fix CTL?
* [+] Create terminal output for external processes (Rqtl1, Rqtl2, pair-scan are done --- WGCNA as a pilot, with @bonfacem and @pjotrp)
* [X] GNQA says there are no results, but has them
* [X] Correlations are slow
## Done
* [X] Rqtl1 - ITP output - 3K individuals - family file
* [X] When bonz is ready wire up GNQA
* + balg-qa.genenetwork.org
* [X] Don't support new PIL - stick to the old one in guix-bioninformatics
* [X] Make GNQA reliable (with @fahamu)
* [X] Improve UX for GNQA (with @shelbys) -- Adrian wants to use our AI UX for their setup
* [X] GNQA add abstracts pubmed (with @shelbys)
=> ../issues/fetch-pubmed-references-to-gnqa
* [X] Edit markdown/gemtext pages through web UI (with @bonfacem)
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