Task updates

4 files changed, 36 insertions, 17 deletions

diff --git a/tasks/alexm.gmi b/tasks/alexm.gmi
index a66de6b..3a4207b 100644
--- a/tasks/alexm.gmi
+++ b/tasks/alexm.gmi
@@ -18,13 +18,16 @@ You can refine the search by constraining the checks some more, e.g. to get high
 
 ## This week
 
-* [ ] Rqtl2 - BXD output work on CD
-* [ ] Rqtl2 - ITP output - 3K individuals - family file
-* [ ] Start application
+* [X] Rqtl2 - BXD output work on CD
+* [X] Rqtl2 - ITP output - 3K individuals - family file
+* [ ] Minor refactorings
+* [ ] Accelerate Xapian functionality
+* [ ] Start application - Pwani
+* [+] Create terminal output for external processes on *PRODUCTION* (Rqtl1, Rqtl2, GEMMA, pair-scan are done --- WGCNA as a pilot, with @bonfacem and @pjotrp)
 
 ## Next week(s)
 
-* [+] Create terminal output for external processes (Rqtl1, Rqtl2, pair-scan are done --- WGCNA as a pilot, with @bonfacem and @pjotrp)
+* [ ] GNQA says there are no results, but has them
 
 ## Done
 
diff --git a/tasks/bonfacem.gmi b/tasks/bonfacem.gmi
index 5445eeb..5c65543 100644
--- a/tasks/bonfacem.gmi
+++ b/tasks/bonfacem.gmi
@@ -10,20 +10,25 @@
 
 ### This week
 
-* [ ] Describe Generif access for Rob in an email
+* [ ] 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. assess porting it to Guix (don't do any work)
-* [ ] Add lmdb output hashes with index and export LMDB_DATA_DIRECTORY
-* [ ] Share small database with @pjotrp and @felixl
+*     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
+* [ ] 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
-* [ ] xapian search, add dataset size keys, as well as GN accession id, trait id, and date
-*     - Improve xapian markdown docs to show all used fields/keys with examples
 * [+] Use aider - give a presentation in the coming weeks
 * [ ] Add case attributes to RDF and share with Felix (depends on @felixl)
 
@@ -64,3 +69,8 @@ Currently closed issues are:
 
 * [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
diff --git a/tasks/felixl.gmi b/tasks/felixl.gmi
index 8e8bfe8..b39ff7b 100644
--- a/tasks/felixl.gmi
+++ b/tasks/felixl.gmi
@@ -10,15 +10,17 @@
 
 #### This week
 
+* [ ] Finalize the slide deck - so it can be read on its own
 * [ ] Analyse and discuss BXD case attributes with Rob --- both group level and dataset level
 * [ ] Sane representation of case attributes in RDF with @bonfacem
-* [ ] Present C.elegans protocol and example mappings with GEMMA/Rqtl
+* [X] Present C.elegans protocol and example mappings with GEMMA/Rqtl
 * [ ] Uploader - setting up code with @fredm
-*     - run small database mysql locally
-*     - aider with Sonnet + code fixes
-*     - document
+*     - [X] run small database mysql locally
+*     - [X] aider with Sonnet + code fixes
+*     - [ ] document - add to code base - merge with Fred's tree - share changes with Pjotr & team
 * [ ] Review paper: one-liners for @pjotrp - why is this important for GN and/or thesis
-* [ ] Sort @alexm application with Pwani
+*     - [ ] list of relevant papers with one-liners - the WHY
+* [ ] Sort @alexm application with Pwani = this week
 
 ### Later weeks
 
diff --git a/tasks/fredm.gmi b/tasks/fredm.gmi
index 5e7e71d..5324285 100644
--- a/tasks/fredm.gmi
+++ b/tasks/fredm.gmi
@@ -1,5 +1,9 @@
 # Tasks for Fred
 
+# Tasks
+
+* [ ] Fix password weakness
+
 ## Description
 
 These are the tasks and issues to be handled by Fred.