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feat: Add a rudimentary ISARIC implementation #1004

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Feb 2, 2023
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@StevenMaude StevenMaude commented Jan 31, 2023

This facilitates access to the ISARIC_New table in TPP for some preliminary work.

We're not entirely sure how the data in there looks yet. When we know, we can substitute for more appropriate types and test examples.

@StevenMaude StevenMaude self-assigned this Jan 31, 2023
@StevenMaude StevenMaude changed the title Add a rudimentary ISARIC implementation feat: Add a rudimentary ISARIC implementation Feb 1, 2023
@StevenMaude StevenMaude force-pushed the steve/isaric branch 2 times, most recently from 62d346b to 3eae5a6 Compare February 1, 2023 14:59
This is to facilitate some exploratory work to query the data with ehrQL.

We don't yet really know what the columns look like,
so let's work with them as all strings for now,
and then later change the types, when we know more.
(The linked data dictionary gives some indication, but it's not clear
how the columns are represented in the database.)

Descriptions taken from:
https://github.com/isaric4c/wiki/blob/d6b87d59a277cf2f6deedeb5e8c1a970dbb970a3/ISARIC/CCP_REDCap_ISARIC_data_dictionary_codebook.pdf
@StevenMaude StevenMaude force-pushed the steve/isaric branch 2 times, most recently from 70c33e3 to 5c79d12 Compare February 1, 2023 16:48
@StevenMaude StevenMaude marked this pull request as ready for review February 1, 2023 16:57
@StevenMaude StevenMaude removed their assignment Feb 1, 2023
And update docs JSON.
databuilder/backends/tpp.py Outdated Show resolved Hide resolved
databuilder/tables/beta/tpp.py Outdated Show resolved Hide resolved
databuilder/tables/beta/tpp.py Outdated Show resolved Hide resolved
On Dave's suggestion; to make it easier to change in future.
We'll later probably want to actually cast these strings as actual
types, but we need to initially know what the data looks like.

If we guess, we're almost certainly going to get one or more columns
wrong, and cause the query to fail.
@StevenMaude StevenMaude merged commit dec86f9 into main Feb 2, 2023
@StevenMaude StevenMaude deleted the steve/isaric branch February 2, 2023 13:44
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2 participants