# Tasks for Munyoki

## Tags

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

## Tasks

### Note
- GN-auth dashboard fixes.  Follow up with Fred.
- Case-attributes used in co-variates.
- Encourage FahamuAI to be open.

### This week
* [+] Case Attributes (Do a diagnostic and delegate)
*     - Git blame.  Add tests.
*     - Error when checking the history.
*     - Reach out to Zach.
*     - Disable diff in the UI.
* [ ] Distinct admin and dev user.
* [ ] Adapter to LMDB into a cross object.
*     - Try computations with R/qtl2.
*     - Look at R LMDB libraries.
*     - Look at functions that read the files.
*     - PJ: LMDB adapter in R and cross-type files.
* [ ] Send Arun an e-mail on how to go about upgrading shepherd.
* [ ] Dump all genotypes from production to LMDB.
*     - PJ sync tux01 genotypes with tux02/04.
* [+] Correlations hash.
*     - Add dataset count to RDF.
* [ ] Spam + LLMs
*     - RateLimiting for Rif Editing.
*     - Honep Pot approach.
* [+] Help Alex with SSL certification container error.
*     - Put the changes in the actual scm files.
* [X] Python Fahamu.
* [X] Memvid - brief look.

### Later
* [ ] Dockerise GN container.   For Harm.
* [ ] Send emails when job fail.
* [ ] Look at updating gn-auth/gn-libs to PYTHONPATH for gn2/3.
* [ ] 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
* [ ] Add case attributes to RDF and share with Felix (depends on @felixl)
* [ ] 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

### 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
* [X] With Alex get rqtl2 demo going in CD (for BXD)
* [X] Set up meeting with ILRI
*     - Zasper https://news.ycombinator.com/item?id=42572057 - Alan
* [X] Migrate fahamuai RAG to VPS and switch tokens to GGI OpenAI account
*     1. Running AI server using (our) VPS and our tokens
*        + Pjotr gives API key - OpenAI - model?
*     2. Read the code base - Elixir is plumbing incl. authentication, Python processing text etc.
*     3. Try ingestion and prompt (REST API) - check out postgres tables
*     4. Backup state from production Elixir
*     5. Assess porting it to Guix (don't do any work) - minimum version Elixir
*     6. Get docs from Shelby/Brian
* [X] Set-up grobit on balg01
*     - guix docker/native
*     - recent breaking changes
* [X] GeneRIF
*     - Merge recent changes first.  Ping Rob.
*     - Brainstorm ideas around log-in.
*     - Unlimited tokens that don't expire.
*     - Sync prod with CD -- sqlite.
*     - Add deletion
* [X] Describe Generif/wikidata access for Rob in an email with test account on CD
*     1. Send email to Rob
*     2. Work on production w. Fred
* [X] Distinguish CD from production -- banners/buttons/colors.
* [X] Use aider - give a presentation in the coming weeks
* [X] gn-auth fixes
* [X] Assess Brian's repo for deployment.
* [X] Finish container work
* - View diffs in BXD: Edit case attributes throws an error.
* [X] Check small db from: https://files.genenetwork.org/database/
* [X] Changes to Production + (Alex)
* [X] File issue with syslog
* [X] LMDB database.
*     - Simplify (focus on small files).  Don't over-rely on Numpy.
* [X] Assess adding GeneRIF to LLM.
* [X] Referrer headers -- a way of preventing bots beyond rate-limiting.