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FIX I2B2 get_consultations_date() #32

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merged 1 commit into from
Feb 8, 2023

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Vincent-Maladiere
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@Vincent-Maladiere Vincent-Maladiere commented Feb 6, 2023

Description

  • Add cache to the BackendDIspatcher
  • Convert note_datetime in get_consultations_date() into str then to datetime to avoid bad date format errors in spark.
  • Extend I2B2 preprocessing from note to note* to include note_deid

Checklist

  • If this PR is a bug fix, the bug is documented in the test suite.
  • Changes were documented in the changelog (pending section).
  • If necessary, changes were made to the documentation (eg new pipeline).

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Codecov Report

Base: 91.89% // Head: 91.89% // Decreases project coverage by -0.01% ⚠️

Coverage data is based on head (2cfa01d) compared to base (e29f4a5).
Patch coverage: 85.71% of modified lines in pull request are covered.

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Additional details and impacted files
@@            Coverage Diff             @@
##             main      #32      +/-   ##
==========================================
- Coverage   91.89%   91.89%   -0.01%     
==========================================
  Files          66       66              
  Lines        2123     2134      +11     
==========================================
+ Hits         1951     1961      +10     
- Misses        172      173       +1     
Impacted Files Coverage Δ
eds_scikit/io/i2b2_mapping.py 12.65% <0.00%> (ø)
eds_scikit/utils/custom_implem/custom_implem.py 87.50% <87.50%> (ø)
eds_scikit/event/consultations.py 98.36% <100.00%> (+0.08%) ⬆️

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@Vincent-Maladiere Vincent-Maladiere marked this pull request as ready for review February 6, 2023 18:04
@Vincent-Maladiere Vincent-Maladiere changed the title FIX I2B2 converters FIX I2B2 get_consultations_date() Feb 6, 2023
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@Thomzoy Thomzoy left a comment

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Nice !
Let's sprinkle bd.cache wherever 🎉

@Thomzoy Thomzoy merged commit 36a9e96 into aphp:main Feb 8, 2023
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3 participants