# 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 * [x] reading metadata from lmdb file using thor * [-] working on reconstructing the genotype files to geno, geno_map and pheno_map file * [x] rate limiting for gnqna users. * [x] check on tokens for no logged in users * [x] Look at isse about signing tokens for non logged in users ## 21/7/2025 * [x] working on reconstructing/reading the genotype files based on bons dumping script * [x] generate and validate cross objects ## 29/7/2025 * [x] adding founder_geno and pheno covariates pheno * [-] minor fixes for lmdb matrix script (missing metadata) * [-] check phenotype work for lmdb ## 4/8/2025 * [-] refactoring lmdb matrix script * [-] integrating fetching rqtl2 from lmdb using bxd as a test pilot ## 11/8/2025 * [x] integrating lmdb genotypes for rqtl2 computation for BXD ## 18/8/2025 * [x] integrating lmdb genotypes for rqtl2 computation for BXD ## 25/8/2025 * [x] script to dump phenotypes and cross metadata to lmdb ## 31/8/2025 * [x] generic script that can parse json cross files and dump the metadata to lmdb * [x] follow up on dumped phenotypes in LMDB for GeneNetwork cc @bons * [x] integrating lmdb rqtl2 adapter to CD (test this on cd for bxd.) ## 23/9/2025 * [x] dumping phenotypes to lmdb (BXDPublish) * [x] dumping cross metadata to lmdb ## 30/9/2025 * [x] profiling and benchmarking read_lmdb_cross against read_cross * [-] Run this on tux02 and integrate to CD ## 7/9/2025 * [-] integrate rqtl2-lmdb adapter to CD cc @bons with directory setup. * [x] improvement on rqtl2-lmdb adapter script; add covariates supports. ## 15/9/2025 * [-] clone qtl2 repo and build rqtl2-lmdb package locally. * [] package rqtl2-lmdb package to guix-bioinformatics. ## 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)