ID Triplet Feature

[cbrinson-rise8]

Description

• Implemenet the ID Triplet as described in RFC-001
• Replace MRN, SSN and DRIVERS_LICENSE with the new IDENTIFIER triplet concept introduced in RFC-001.

Related Issues

closes #125

Additional Notes

• Update the /link endpoint to accept an identifier triplet
• Create blocking values on IDENTIFIER values
• Feature match on IDENTIFIER and/or IDENTIFIER:XXX values
• Add new test cases for blocking and feature matching on the new values
• Update documentation in references.md regarding the new blocking key and feature

<--------------------- 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.
• The changes implement the desired functionality or fix the reported issue.
• The tests cover the new changes and pass successfully.
• Any potential edge cases or error scenarios have been considered.

[codecov]

Codecov Report

Attention: Patch coverage is 96.29630% with 9 lines in your changes missing coverage. Please review.

Project coverage is 96.92%. Comparing base (c07aea2) to head (3c8121e).
Report is 2 commits behind head on main.

Files with missing lines	Patch %	Lines
src/recordlinker/schemas/pii.py	87.69%	8 Missing ⚠️
src/recordlinker/schemas/identifier.py	99.40%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #146      +/-   ##
==========================================
- Coverage   97.21%   96.92%   -0.29%     
==========================================
  Files          30       31       +1     
  Lines        1327     1496     +169     
==========================================
+ Hits         1290     1450     +160     
- Misses         37       46       +9     

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[ericbuckley]

Good start @cbrinson-rise8

[ericbuckley]

Chaning Feature from an enum to a pydantic.BaseModel means we can't auto list out all the choices in the API docs anymore for features. Since we already have an enum for the FeatureAttribtues and another for Identifier, did you consider just combining those to create a new Feature enum? For example

def all_features() -> typing.Iterator[str]:
    """
    Return a list of all possible features that can be used for comparison.
    """
    for feature in FeatureAttribute:
        yield str(feature)
        if feature == FeatureAttribute.IDENTIFIER:
            for identifier in IdentifierType:
                yield f"{feature}:{identifier}"
Feature = enum.Enum("Feature", [(f, f) for f in all_features()])

[cbrinson-rise8]

Added in an enum for this

[ericbuckley]

Let me share a slightly different implementation. I'm thinking we don't need both Feature and FeatureEnum, we can just use one class for both functionality and docs. I'm not married to this implementation as it requires us to "parse" everytime we call suffix() or attribute(), so it might be better to split the suffix and attribute in the constructor so we don't have to parse everytime the functions are invoked. However this should give you a better idea as how we can meet both needs with one class.

class Feature(enum.Enum):
    """
    Enum for the different Patient attributes that can be used for comparison.
    """

    # Dynamically populate the enum members
    @classmethod
    def populate(cls):
        """Populate the Feature enum dynamically."""
        features = {}
        for f in FeatureAttribute:
            features[f.value] = f.value
            if f == FeatureAttribute.IDENTIFIER:
                for i in IdentifierType:
                    features[f"{f.value}:{i.value}"] = f"{f.value}:{i.value}"
        # Add members to the class
        cls._member_map_.update(features)
        cls._value2member_map_.update({v: cls(k, v) for k, v in features.items()})

    def attribute(self) -> FeatureAttribute:
        """Get the attribute of the feature."""
        return FeatureAttribute(self.value.split(":")[0])

    def suffix(self) -> typing.Optional[IdentifierType]:
        """Get the suffix of the feature if it is an identifier, otherwise None."""
        if self.attribute() == FeatureAttribute.IDENTIFIER:
            return IdentifierType(self.value.split(":")[1])
        return None

    def __str__(self):
        """Return the value of the enum as a string."""
        return self.value
Feature.populate()

[ericbuckley]

MRN and SSN on lines 18 and 22 need to be removed as well