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Diffstat (limited to 'tasks/alexm.gmi')
| -rw-r--r-- | tasks/alexm.gmi | 89 |
1 files changed, 89 insertions, 0 deletions
diff --git a/tasks/alexm.gmi b/tasks/alexm.gmi index 7ec8e87..e410046 100644 --- a/tasks/alexm.gmi +++ b/tasks/alexm.gmi @@ -75,6 +75,95 @@ You can refine the search by constraining the checks some more, e.g. to get high * 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 |
