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core: add core__diagnosticreport table #322

Merged
merged 3 commits into from
Dec 4, 2024
Merged

core: add core__diagnosticreport table #322

merged 3 commits into from
Dec 4, 2024

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mikix
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@mikix mikix commented Dec 3, 2024

Checklist

  • Consider if documentation in docs/ needs to be updated
    • If you've changed the structure of a table, you may need to run generate-md
    • If you've added/removed core study fields that not in US Core, update our list of those in core-study-details.md
  • Consider if tests should be added
  • Update template repo if there are changes to study configuration in manifest.toml

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github-actions bot commented Dec 3, 2024

☂️ Python Coverage

current status: ✅

Overall Coverage

Lines Covered Coverage Threshold Status
2314 2306 100% 90% 🟢

New Files

File Coverage Status
cumulus_library/studies/core/builder_diagnosticreport.py 100% 🟢
TOTAL 100% 🟢

Modified Files

File Coverage Status
cumulus_library/builders/counts.py 100% 🟢
cumulus_library/builders/statistics_templates/counts_templates.py 100% 🟢
cumulus_library/studies/core/count_core.py 100% 🟢
TOTAL 100% 🟢

updated for commit: 1f03765 by action🐍

@mikix mikix force-pushed the mikix/diagnostics branch 2 times, most recently from 4252a56 to 45c899a Compare December 3, 2024 21:38
pyproject.toml Show resolved Hide resolved
@mikix mikix force-pushed the mikix/diagnostics branch from 45c899a to 1fb444c Compare December 3, 2024 21:40
@mikix mikix changed the title WIP: core: add core__diagnosticreport table core: add core__diagnosticreport table Dec 3, 2024
@mikix mikix marked this pull request as ready for review December 3, 2024 22:03
Comment on lines 4 to 15
-- This table includes all fields of interest to the US Core DiagnosticReport profiles.
-- EXCEPT FOR:
-- * the 'presentedForm' field, which is an attachment array that is stripped out by the ETL.
-- * the `reporter` field, simply due to it not likely being interesting to consumers
-- and being an array field, which would require a lot of row duplication.
--
-- US Core profiles for reference:
-- * https://hl7.org/fhir/us/core/STU4/StructureDefinition-us-core-diagnosticreport-lab.html
-- * https://hl7.org/fhir/us/core/STU4/StructureDefinition-us-core-diagnosticreport-note.html
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oh what a nice piece of documentation that we should replicate across all the main core templates

@mikix mikix force-pushed the mikix/diagnostics branch from 1fb444c to 0c01575 Compare December 4, 2024 16:05
@mikix mikix merged commit dd41536 into main Dec 4, 2024
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@mikix mikix deleted the mikix/diagnostics branch December 4, 2024 17:02
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2 participants