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Create New Parsers Framework #102

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merged 4 commits into from
Oct 30, 2024
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@cbrinson-rise8 cbrinson-rise8 commented Oct 29, 2024

Description

Abstract the parsing of FHIR out into its own module, as the linking algorithm should be input format agnostic. This approach will let us expand our supported formats for ELR and eCR ahead.

Related Issues

closes #80

Additional Notes

  • creates recordlinker.parsers.fhir
  • add new link/fhir endpoint that accepts fhir bundles but response similar to the /link endpoint
  • add tests for new endpoint and new test file for fhir parser

<--------------------- REMOVE THE LINES BELOW BEFORE MERGING --------------------->

Checklist

Please review and complete the following checklist before submitting your pull request:

  • I have ensured that the pull request is of a manageable size, allowing it to be reviewed within a single session.
  • I have reviewed my changes to ensure they are clear, concise, and well-documented.
  • I have updated the documentation, if applicable.
  • I have added or updated test cases to cover my changes, if applicable.
  • I have minimized the number of reviewers to include only those essential for the review.

Checklist for Reviewers

Please review and complete the following checklist during the review process:

  • The code follows best practices and conventions.
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codecov bot commented Oct 29, 2024

Codecov Report

Attention: Patch coverage is 85.00000% with 9 lines in your changes missing coverage. Please review.

Project coverage is 95.18%. Comparing base (65f9563) to head (a869162).
Report is 2 commits behind head on main.

Files with missing lines Patch % Lines
src/recordlinker/hl7/fhir.py 82.85% 6 Missing ⚠️
src/recordlinker/routes/link_router.py 88.00% 3 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #102      +/-   ##
==========================================
- Coverage   95.33%   95.18%   -0.16%     
==========================================
  Files          24       25       +1     
  Lines        1158     1183      +25     
==========================================
+ Hits         1104     1126      +22     
- Misses         54       57       +3     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

@cbrinson-rise8 cbrinson-rise8 force-pushed the feat/new-parsers-framework branch from 3a50035 to 8a81f1b Compare October 29, 2024 20:16
@cbrinson-rise8 cbrinson-rise8 marked this pull request as ready for review October 29, 2024 20:27
@cbrinson-rise8 cbrinson-rise8 self-assigned this Oct 30, 2024
@cbrinson-rise8 cbrinson-rise8 mentioned this pull request Oct 30, 2024
9 tasks
@cbrinson-rise8 cbrinson-rise8 force-pushed the feat/new-parsers-framework branch 2 times, most recently from a259801 to 2c8747e Compare October 30, 2024 18:25
@cbrinson-rise8 cbrinson-rise8 force-pushed the feat/new-parsers-framework branch from 2c8747e to 6402536 Compare October 30, 2024 18:41
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@ericbuckley ericbuckley left a comment

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@cbrinson-rise8 looks great, just made 1 small change to a docstring

@cbrinson-rise8 cbrinson-rise8 merged commit 800265a into main Oct 30, 2024
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@cbrinson-rise8 cbrinson-rise8 deleted the feat/new-parsers-framework branch October 30, 2024 19:45
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create new parsers framework
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