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feat: add our I2B2 to OMOP converter #21

Merged
merged 7 commits into from
Jan 19, 2023
Merged

feat: add our I2B2 to OMOP converter #21

merged 7 commits into from
Jan 19, 2023

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Vincent-Maladiere
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Description

Add I2B2 converter methods from EDSTeva with small revamps. The get_i2b2_table method is used by HiveData during table fetching to perform table and column renaming, along with some value changes.
I need to test it on our I2B2 data.

TODO:

  • Test with our I2B2 extract. First, manually on a single table, then extend the analysis and find areas we don't cover yet. Ideally, we'll have a script to quantify the discrepancies.
  • We need to document it. We want this feature to be user-facing, so we'll need thorough documentation, examples, and contributing guidelines.
  • How to write tests on that? Maybe running the script manually at first?

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).

@codecov-commenter
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codecov-commenter commented Jan 5, 2023

Codecov Report

Base: 94.95% // Head: 92.54% // Decreases project coverage by -2.40% ⚠️

Coverage data is based on head (b4b8f58) compared to base (e75d7fc).
Patch coverage: 22.38% of modified lines in pull request are covered.

Additional details and impacted files
@@            Coverage Diff             @@
##             main      #21      +/-   ##
==========================================
- Coverage   94.95%   92.54%   -2.41%     
==========================================
  Files          63       64       +1     
  Lines        1963     2026      +63     
==========================================
+ Hits         1864     1875      +11     
- Misses         99      151      +52     
Impacted Files Coverage Δ
eds_scikit/io/i2b2_mapping.py 13.33% <13.33%> (ø)
eds_scikit/io/hive.py 100.00% <100.00%> (ø)
eds_scikit/io/settings.py 100.00% <100.00%> (ø)
eds_scikit/emergency/emergency_care_site.py 90.00% <0.00%> (-0.33%) ⬇️
eds_scikit/icu/icu_care_site.py 100.00% <0.00%> (ø)
eds_scikit/structures/description.py 100.00% <0.00%> (ø)
eds_scikit/emergency/emergency_visit.py 100.00% <0.00%> (ø)

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@Vincent-Maladiere
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Pushing it now to master to ease testing on k8

@Vincent-Maladiere Vincent-Maladiere merged commit b841ef2 into main Jan 19, 2023
@Vincent-Maladiere Vincent-Maladiere deleted the i2b2_plugin branch January 19, 2023 11:00
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2 participants