# Tasks for Munyoki

## Tags

* kanban: bonfacem
* assigned: bonfacem
* status: in progress

## Tasks

### This week

* [ ] Describe Generif/wikidata access for Rob in an email with test account on CD
*     1. Send email to Rob
*     2. Work on production
* [ ] Migrate fahamuai RAG to VPS and switch tokens to GGI OpenAI account
*     1. Running AI server using (our) VPS and our tokens
*     2. Read the code base
*     3. Try ingestion and prompt (REST API)
*     4. Backup state from production Elixir
*     5. Assess porting it to Guix (don't do any work) - minimum version Elixir
* [ ] xapian search, add dataset size keys, as well as GN accession id, trait id, and date/year
*     - Improve xapian markdown docs to show all used fields/keys with examples
*     - genewiki search (link in table? check with Rob)
*     - base line with GN1 search - add tests
*     - Fix missing search term for sh* - both menu search and global search
*     - Use GN1 as a benchmark for search results (mechanical Rob?)
*     - Xapian ranges for markers
* [ ] With Alex get rqtl2 demo going in CD (for BXD)

### Later

* [ ] Sample/individual/strain/genometype counts for PublishData only - ProbeSetData? https://github.com/genenetwork/genenetwork2/blob/testing/scripts/sample_count.py - mirror in RDF and use global search
*     - search for all traits that have more than X samples
* [+] Use aider - give a presentation in the coming weeks
* [ ] Add case attributes to RDF and share with Felix (depends on @felixl)

### Even later

* [ ] Rest API for precompute output (mapping with GEMMA)
* [ ] GNQA add GN metadata (to RAG)
*     - Focus on RIF
*     - triple -> plain text
*     - bob :fatherof nancy -> Bob is the father of Nancy.

## Later

* [ ] AI improvements

### On going tasks

=> https://issues.genenetwork.org/search?query=assigned%3ABonfaceKilz+AND+is%3Aopen+AND+status%3Ain-progress&type=all All in-progress tasks

### Stalled (To Be Done/Completed)

=> https://issues.genenetwork.org/search?query=assigned%3ABonfaceKilz+AND+tag%3Astalled+AND+is%3Aopen&type=open-issueo All stalled taskse that are to be promoted to in-progress

### Unclear Issues

Ad-hoc issues that were picked some where some how:

=> https://issues.genenetwork.org/search?type=open-issue&query=assigned%3ABonfaceKilz%20AND%20NOT%20tag%3Astalled%20AND%20NOT%20tag%3Ain-progress%20AND%20status%3Aunclear%20OR%20priority%3Aunclear Unclear Issues


### Closed Issues

Should something in one of these closed issues be amiss, we can always and should re-open the offending issue.

Currently closed issues are:

=> https://issues.genenetwork.org/search?type=closed-issue&query=assigned%3ABonfaceKilz%20AND%20type%3Aissue%20AND%20is%3Aclosed Closed Issues

* [X] Indexing generif data / Improve Local Search
* [X] lmdb publishdata output and share with Pjotr and Johannes

## Done

* [X] Add lmdb output hashes with index and export LMDB_DATA_DIRECTORY
* [X] Share small database with @pjotrp and @felixl