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# 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
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