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| -rw-r--r-- | topics/meetings/jnduli_bmunyoki.gmi | 48 |
1 files changed, 43 insertions, 5 deletions
diff --git a/topics/meetings/jnduli_bmunyoki.gmi b/topics/meetings/jnduli_bmunyoki.gmi index 73b48d5..81bb5d2 100644 --- a/topics/meetings/jnduli_bmunyoki.gmi +++ b/topics/meetings/jnduli_bmunyoki.gmi @@ -1,5 +1,41 @@ # Meeting Notes +## 2024-06-18 +### Agenda + +* Last week review: DONE, made good progress on what we planned. We need to make sure we're more aware of the TODOs we had. +* Plan for this week: DONE, LET'S GOOO! +* Reviewing patches: added to week's goals. +* Search bugs discussions: Boni will create an issue with all details and we'll plan further on how to attack this. + +If we have a plan for the week, and something comes up that breaks our plan: + +* Are we aware that it broke our plans? +* Communicate the impact this may have on the plan. + +### Plan for Week + +* TODO: @bmunyoki rebuild guix container with new mcron changes +* TODO: @jnduli attempts to make UI change that shows all supported keys in the search +* TODO: @bmunyoki create an issue with all the problems experienced with search and potential solutions. Make sure it has replication steps, and plans for solutions. +* TODO: @bmunyoki follows up to make sure RDF changes are visible in production and fix issues that come up +* TODO: @bmunyoki and @jnduli genewiki indexing +* TODO: @bmunyoki demoes and documents how to run and test guix cron job for indexing +* TODO: @bmunyoki trains @jnduli on how to review patchsets from emails +* TODO: @jnduli attempts to add stronger types to index-genenetwork script, to make it explicit that we're using MonadicDicts +* TODO: @jnduli Documentation improvements for GN2 and GN3 and auth? None done last week. +* TODO: @jnduli Follow up notes on setting up local index-genenetwork search + + +Nice to haves: + +* TODO: minor: bonfacem makes sure that mypy in CI runs against the index-genenetwork script. +* TODO: @bmunyoki improve search documentation and fix bugs in the frontend: binary term search doesn't work as expected +* TODO: @bmunyoki follow up with Rob to makes sure he tests search after everything is complete +* TODO: @bmunyoki follow up how do we make sure that xapian prefix changes in code retrigger xapian indexing? + + + ## 2024-06-11 ### Agenda @@ -10,6 +46,7 @@ In gn3, make sure to run: > pylint main.py setup.py wsgi.py setup_commands tests gn3 scripts > TODO jnduli run this: mypy --show-error-codes . + DONE: led to a PR that fixed all mypy errors in index-genenetwork > pytest -k unit_test * Set up new DB before sync + fixing any problems that occur: DONE, no errors after Jnduli set up new DB. @@ -19,13 +56,14 @@ In gn3, make sure to run: * Probeset data exists in SQL. Generif metadata exists in RDF. * Write code that queries RDF for Generif metadata and enriches exising Probeset query. * DONE: checksums in Generif rdf output -* TODO: jnduli look at xapian docs and their example for python bindings -* TODO: bonfacem makes sure tux02 indexing works -* TODO: bonfacem make changes to mcron and guix-machines. +* TODO: jnduli look at xapian docs and their example for python bindings: DONE, led to a WIP PR for wiki data indexing and a local custom script to search the index without the need to run genenetwork web service +* TODO: bonfacem makes sure tux02 indexing works: DONE, there's a working patchset sent to Arun for review. +* TODO: bonfacem make changes to mcron and guix-machines: DONE, there's a working patch set sent to Arun. Follow up needs to be done for the learnings gained + ### How would GeneWiki work? * GeneWiki = GeneRif data from NCBI * Workflow would be similar to Generif Indexing. We need to figure out if we'll need an extra RDF query or if we can modify the existing SPARQL query. -* TODO: jnduli attempts to add stronger types to index-genenetwork script, to make it explicit that we're using MonadicDicts. -* TODO: bonfacem makes sure that mypy in CI runs against the index-genenetwork script. +* TODO: jnduli attempts to add stronger types to index-genenetwork script, to make it explicit that we're using MonadicDicts: Not DONE, got stuck trying to run index-genenetwork locally and removing global variables from the script.. +* TODO: bonfacem makes sure that mypy in CI runs against the index-genenetwork script: NOT DONE, needs a separate PR that will be sent to Arun. |