# Weekly meetings

In this document we will track tasks based of our weekly meetings. This list sets the agenda
on progress for the next week's meeting.

## 02-10-2024
## @felixm
* [ ] Use Aider to contribute and cover to Fred's coding.  Share useful prompts.
* [ ] Feed relevant papers to GPT and find similar summary for other datasets.  Start with C-Elegans.


## @bonfacem
* [ ] Share values with PJ.
* [ ] Assume LMDB files are transient.  When hash doesn't exist, generate the hash for that dataset.  Use LMDB to store key value pairs of hashes.
* [ ] Add dump script to gn-guile.
* [ ] Add Case Attributes in Virtuoso.

## @alex
* [ ] Push R/QTL2 to production
* [ ] Have R/QTL2 work for ITP

Nice to have:
* Think about editing publish data and consequent updates to LMDB.

## @pjotr
* Kickstart UTHSC VPN access for Felix and Alex.

## 01-20-2024
### @bonfacem

* [ ] Report:    OpenAI on Aider - use AI for programming - discuss with @alexm

=> https://issues.genenetwork.org/topics/ai/aider

* [-] Metadata:  Provide list of case attributes for BXD to @flisso
* [-] Code UI:   GeneRIF and GenWiki should work from the mapping page - encourage people to use
                 - anyone logged in can edit
                 - If RIF does not exist point to GeneWiki
                 - If GeneWiki does not exist provide edit page
* [ ] Code export: Exporting traits to lmdb PublishData - @alexm helps with SQL
                 - missing data should not be an X
                 - run lmdb design (first code) by @pjotrp
                 - start exporting traits for Johannes (he will need to write a python reader)
* Later:         Improve the work/dev container for @alexm

### @flisso

* [ ] Write:  Uploader protocol.  NOTES: Finished with C-elegans.  Yet to test with other datasets.
* [ ] Script: Run Reaper
* [ ] Data:   Case attributes - with @bonfacem
* [ ] Write:  Create protocol to upload case attributes

### @alexm

* [ ] Code: Rqtl2 match Rqtl1: match scan changes.  Notes: PR out and added tests.
* [ ] Bug:  Fix pair scan.  NOTES: Fixed it.  But can't test it now since CD is down.
* Later: AI changes

### @Pjotr

* [ ] Code: Work on precompute with GEMMA (w. Jameson)
* [ ] Code: Take Bonface's trait files when they become available


## 01-27-2024

Last week's error with CD and production downtime:
* [ level 1] Container: Error messages when data not loaded in Virtuoso, Indexing.
* [ level 2] Sheepdog: Check services --- sheepdog.  Health checkpoints.
* [ level 3] User feedback.  Escalate errors correctly to the users, so they can report to coders

### @bonfacem
* [ ] Troubleshoot CD.
* [ ] Export files in lmdb.  Yohannes read file in Python example
* [ ] Metadata:  Provide list of case attributes for BXD to @flisso
* [ ] Aider: See if it can generate some guile and python.  Give an example.

### @alexm
* [ ] UI for R/Qtl2.

### @flisso
* [ ] Look at Fred Python code for the uploader and report on this.