Use imaging UID from OMOP-ES extract

[milanmlft]

Description

Related to https://github.com/UCLH-Foundry/the-rolling-skeleton/issues/161
I suspect this has to wait until https://github.com/UCLH-Foundry/the-rolling-skeleton/issues/161 is done and the OMOP-ES extracts actually contain the study UIDs.

• Get Study UID from OMOP-ES extract
• Use the Study UID to query the VNA initially, fall back to MRN + accession number if not available
• Add the UID to the PIXL database Image model and use for querying during anonymisation

Also cleaned up the pixl_dcmd tests and fixtures a bit, as I was getting confused where all the hardcoded values were coming from.

Type of change

Please delete options accordingly to the description.

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• This change requires a documentation update

Suggested Checklist

• I have performed a self-review of my own code.
• I have made corresponding changes to the documentation.
• My changes generate no new warnings.
• I have commented my code, particularly in hard-to-understand areas.
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• Make sure your branch is up-to-date with main branch. See CONTRIBUTING for a general example to syncronise your branch with the main branch.
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[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 83.02%. Comparing base (6eb8750) to head (cfe755e).

Additional details and impacted files

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- Coverage   84.11%   83.02%   -1.10%     
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  Files          83       80       -3     
  Lines        3545     3352     -193     
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- Hits         2982     2783     -199     
- Misses        563      569       +6     

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[stefpiatek]

Looking good, tests are catching some errors. UIDs are in omop es, so you can ask Baptiste to set off a pinpoint run again if you want to test on real data

[stefpiatek]

Looking glorious thanks!

I wonder for pinpoint we could just delete all rows which haven't been exported and then run populate so the UIDs will exist in the ones its still trying to export. From thereon in, we wouldn't expect the UID to change so that should be fine

[milanmlft]

I wonder for pinpoint we could just delete all rows which haven't been exported and then run populate so the UIDs will exist in the ones its still trying to export. From thereon in, we wouldn't expect the UID to change so that should be fine

Sounds reasonable!