4.7 KiB
Plan/Todo [2025-01-06]
Goal is to update the main images with more details, i.e. adding means etc.
- get aact_db back up
- attach it to a "research" network
- restart rocker, attaching it to the same research network.
NOTES
aact_db-restored-2024-11-27 didn't successfully restore. It is missing all the important stuff.
Figured out why the restore was failing. My code to restore had a faulty check to see if the DB was up and ready. Fixed that now.
Waiting for restore (manually triggered) to start. Then I should have access to the table as needed.
It seems like I'm missing some data within a schema, specifically the Formularies and their associated views.
My options are:
- search around for documentation or other stuff
- try to rebuild
my suspision is that I forgot to back it up. I think it is probably worth looking for. - So I've been looking through my copy of ClinicalTrialsDataProcessing, and have not found anything referencing it. The formularies data is required for my analysis though. If I remember correctly, I manually uploaded the USP datasets in DBeaver, then created any views etc.
I think that I'll have to recreate it. This is going to be hard because I'm not sure what it did. At least I created mildly informative table names.
The tables/views I've identified are: -
Formularies.nct_to_brands_through_uspdc
It looks like I need to - import usp-dc dataset - link those drugs to usp data - create a view that links those automatically - back it up. - double check the data I get from the request.
The links will be through RXCUIs, and grouped on USP Class In effect,
for a given RXCUI, I want to get the list of RXCUI's which have the same
USP-DC class, and then be able to link back to brands.
This should have the following links: - RXCUI -> USP-DC category/class pair - USP-DC category/class pair -> RXCUIs - RXUCIs -> competitors
Do I want to combine the USP-DC and UPS-MMG datasets? No, there is enough difference in them that I don't want to have to handle it that way.
I've been working on this in scripts/ConfiguringFormularies.sql
So what I've managed to do so far is export tables, backup the data.
I've got a version that connects trials to brand names, but there may be more details to the connection than I thought. I'd like to check if I need to filter anything or check if there are other ingredients etc that I need to include. */I probably need to write some descriptions of all the tables and views to put everything together. An ai would probably be helpful in doing this./*
Code snippets
podman run \
-e POSTGRES_PASSWORD="${POSTGRES_PASSWORD}" \
-e POSTGRES_USER="${POSTGRES_USER}" \
-e POSTGRES_DB="${POSTGRES_DB}" \
--name "${CONTAINER_NAME}" \
--detach \
--network research-network \
--shm-size=512mb \
--volume ./backup/:/backup/ \
-p 5432:5432\
postgres:14-alpine
function check_postgres {
podman exec -i "${POSTGRES_DB}" psql -h localhost -U "${POSTGRES_USER}" -d "${POSTGRES_DB}" -c '\q' > /dev/null 2>&1
}
Notes at end of day
- was reasonably productive in getting stuff unblocked for finishing JMP, which i'll need to do before I leave town next week.
What I've got to do tomorrow
I've got a version that connects trials to brand names, but there may be more details to the connection than I thought. I'd like to check if I need to filter anything or check if there are other ingredients etc that I need to include. */I probably need to write some descriptions of all the tables and views to put everything together. An ai would probably be helpful in doing this./* At the end of it all, I should be able to get a count of competing drugs per trial.
Once that is done, I can relink aact_db and rocker, then rerun my analysis. Then I can adjust the images that I need for my JMP.
[2025-01-07 Tue 12:01] notes
So what I've got to do is
DONE Investigate what compounds are showing up in my current list
if that is what I want, then I'll be able proceed with redoing my images if not, then I'll have to work on adjusting the views etc that I have.
I've looked through it and it seems to correct.
ConfiguringFormularies.sql:81 [2025-01-07 Tue 13:24]
I've tweaked these three views to make them clearer.
I also renamed the view of interest to "Formularies".nct_to_brand_counts_through_uspdc to better represent what it does.
TODO Rerun the analysis
So it looks like I'll need to
- take a backup of aact_db
- restore from backup, putting the container in the research network
- then rerun the analysis.
TODO Add more details to images
This should include means and some quantiles