# 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

* [] implementation for  no logim 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 


## 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)