Adding Category data to Conditions table

[robertandremitchell]

PULL REQUEST

Summary

This adds a new column to the conditions table, category. This is an organizational structure that we need to organize our conditions to display like so: https://www.figma.com/design/Iuw9me6kYftBF4WTCEsCZz/Query-Connector?node-id=475-18708&node-type=frame&t=Lcg6TdahnUvYPBsR-0

These are the categories we would end up with:

the three missing are ones we added. Here are my thoughts on how to handle:

• Social Determinants of Health, which I believe we can remove from the DB given convo today
• Cancer (Leukemia), which, probably fairly reasonably, could be coded to coded to be included in the Cancer category.
• Newborn Screening, which could be Birth Defects and Infant Disorders? I don't see an immediately obvious one we would nest Newborn Screening under, otherwise. I can see an argument for it being standalone.

a few backend considerations: right now, we are just using INSERT statements to create the temporary category_data table that needs to be merged with conditions.

Other ideas:

• this data in theory is only necessary for the display of data on the custom query page. We could just have a small script that transforms this into a JSON we reference to functionally display this data independent of the db.
• we could read the data from an S3 bucket. This is probably a lot more work, but if we were uncomfortable committing this file as a standalone file to the repo, or if it introduces Terraform complications, that might provide some balance.

  Related Issue

Fixes #68

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Checklist

• [ ] If this code affects the other scrum team, have they been notified? (In Slack, as reviewers, etc.)

[robertandremitchell]

Looks fine to me as is, though I would probably be in the camp of just using INSERT statements to make that temporary table. I have no problem exposing this file publicly, but we probably aren't looking to do so. Mounting and S3 both seem like overkill to me, but that's more a stylistic and preference thing, I think--I would rather our DB product not establish the pattern of bringing in externally mounted volumes. I think the seeding/creation should be as self-contained as possible. I don't feel strongly either way, and I don't think anything here is blocking though!

I'm torn, I think I lean toward a bunch of INSERT statements also being fine. I think I'd probably want to add a script that can parse this CSV to write those INSERTs each time a new eRSD drops for some future-proofing (or, preferably, convince APHL to surface this data in the eRSD...).

happy to look into that option if we think it's cleaner.

[DanPaseltiner]

@bamader definitely agree that ultimately all database creation should be handled in a single place (the work you and @m-goggins are doing). I totally forgot about this when reviewing. I'd propose that we move this along so that @robertandremitchell and @fzhao99 aren't blocked on their query building work, but eventually have this along with all other seeding handled at the app layer.

[bamader]

@DanPaseltiner That sounds good to me--approving with the idea that we revisit the conversation during broader DB creation!

[robertandremitchell]

@bamader definitely agree that ultimately all database creation should be handled in a single place (the work you and @m-goggins are doing). I totally forgot about this when reviewing. I'd propose that we move this along so that @robertandremitchell and @fzhao99 aren't blocked on their query building work, but eventually have this along with all other seeding handled at the app layer.

Makes sense to me. I've created a new issue in the backlog so that we don't lose track of that work (https://linear.app/skylight-cdc/issue/QUE-43/refactor-conditionscategory-migration), but I will work on getting this merged shortly (darn CI tests).

Thank you both for your review!

[robertandremitchell]

requesting a re-review since switching to INSERT over CSV. everything else should be the same.