DRAFT: adding biology support to i2b2 connector

[Thomzoy]

Description

Adapts the existing i2b2 connector to handle biology data

• Strips prefix LAB: from codes
• Adds LOINC concepts
• Adds ANABIO to LOINC codes by using data from eds_scikit_aphp

Checklist

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

[codecov-commenter]

Codecov Report

Base: 92.77% // Head: 91.89% // Decreases project coverage by -0.89% :warning:

Coverage data is based on head (35a662e) compared to base (b841ef2). Patch coverage: 51.92% of modified lines in pull request are covered.

:exclamation: Current head 35a662e differs from pull request most recent head bb51963. Consider uploading reports for the commit bb51963 to get more accurate results

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Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #27 +/- ## ========================================== - Coverage 92.77% 91.89% -0.89% ========================================== Files 66 66 Lines 2105 2123 +18 ========================================== - Hits 1953 1951 -2 - Misses 152 172 +20 ``` | [Impacted Files](https://codecov.io/gh/aphp/eds-scikit/pull/27?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=aphp) | Coverage Δ | | |---|---|---| | [eds\_scikit/emergency/emergency\_care\_site.py](https://codecov.io/gh/aphp/eds-scikit/pull/27?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=aphp#diff-ZWRzX3NjaWtpdC9lbWVyZ2VuY3kvZW1lcmdlbmN5X2NhcmVfc2l0ZS5weQ==) | `93.54% <ø> (+3.22%)` | :arrow_up: | | [eds\_scikit/io/files.py](https://codecov.io/gh/aphp/eds-scikit/pull/27?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=aphp#diff-ZWRzX3NjaWtpdC9pby9maWxlcy5weQ==) | `100.00% <ø> (ø)` | | | [eds\_scikit/io/hive.py](https://codecov.io/gh/aphp/eds-scikit/pull/27?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=aphp#diff-ZWRzX3NjaWtpdC9pby9oaXZlLnB5) | `100.00% <ø> (ø)` | | | [eds\_scikit/io/settings.py](https://codecov.io/gh/aphp/eds-scikit/pull/27?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=aphp#diff-ZWRzX3NjaWtpdC9pby9zZXR0aW5ncy5weQ==) | `100.00% <ø> (ø)` | | | [eds\_scikit/io/i2b2\_mapping.py](https://codecov.io/gh/aphp/eds-scikit/pull/27?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=aphp#diff-ZWRzX3NjaWtpdC9pby9pMmIyX21hcHBpbmcucHk=) | `12.65% <7.69%> (-0.68%)` | :arrow_down: | | [eds\_scikit/biology/viz/wrapper.py](https://codecov.io/gh/aphp/eds-scikit/pull/27?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=aphp#diff-ZWRzX3NjaWtpdC9iaW9sb2d5L3Zpei93cmFwcGVyLnB5) | `85.29% <66.66%> (ø)` | | | [eds\_scikit/biology/cleaning/cohort.py](https://codecov.io/gh/aphp/eds-scikit/pull/27?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=aphp#diff-ZWRzX3NjaWtpdC9iaW9sb2d5L2NsZWFuaW5nL2NvaG9ydC5weQ==) | `88.88% <100.00%> (ø)` | | | [eds\_scikit/biology/cleaning/transform.py](https://codecov.io/gh/aphp/eds-scikit/pull/27?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=aphp#diff-ZWRzX3NjaWtpdC9iaW9sb2d5L2NsZWFuaW5nL3RyYW5zZm9ybS5weQ==) | `100.00% <100.00%> (ø)` | | | [eds\_scikit/biology/utils/process\_concepts.py](https://codecov.io/gh/aphp/eds-scikit/pull/27?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=aphp#diff-ZWRzX3NjaWtpdC9iaW9sb2d5L3V0aWxzL3Byb2Nlc3NfY29uY2VwdHMucHk=) | `96.71% <100.00%> (ø)` | | | [eds\_scikit/biology/utils/process\_measurement.py](https://codecov.io/gh/aphp/eds-scikit/pull/27?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=aphp#diff-ZWRzX3NjaWtpdC9iaW9sb2d5L3V0aWxzL3Byb2Nlc3NfbWVhc3VyZW1lbnQucHk=) | `96.77% <100.00%> (ø)` | | | ... and [5 more](https://codecov.io/gh/aphp/eds-scikit/pull/27?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=aphp) | | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=aphp). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=aphp)

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