File n3c_mapping_conversion.py has 309 lines of code (exceeds 250 allowed). Consider refactoring.

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#!/usr/bin/env python
# -*- coding: utf-8 -*-


# import needed libraries

File analytic_utils.py has 291 lines of code (exceeds 250 allowed). Consider refactoring.

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#!/usr/bin/env python
# -*- coding: utf-8 -*-

"""
Analytic Utility Functions.

Function process_mapping_evidence has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.

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def process_mapping_evidence(evidence_list):
    evidence_dict = {'all': [], 'dbxref': [], 'synonym': [], 'label': [], 'similarity': []}

    for x in evidence_list:
        for i in x.split(' | '):

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Function main has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

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def main():

    ### Step 0: set/update hard-coded variables
    # update hard-coded attributes
    version = 'v2.0.0'

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Function splits_concept_levels has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.

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def splits_concept_levels(data: pd.DataFrame, type_col: Optional[str], concept_strings: List) -> List:
    """Takes a Pandas DataFrame and a string containing a keyword and with the keyword, splits the input DataFrame
    into concept and ancestor-level data. The keyword is used to obtain relevant columns where the data differs for
    concepts and ancestors.

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Function process_error_analysis_data has 5 arguments (exceeds 4 allowed). Consider refactoring.

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def process_error_analysis_data(error_analysis, purposefully_unmapped, missing_concepts, cp_data, chco_data):

Function ontology_loader has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

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    def ontology_loader(self) -> None:
        """Function takes a list of file paths to pickled data, loads the data, and then saves each file as a dictionary
        entry.

        Returns:

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Function downloads_data_from_url has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

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    def downloads_data_from_url(self, owltools_location: str = './omop2obo/libs/owltools') -> None:
        """Takes a string representing a file path/name to a text file as an argument. The function assumes
        that each item in the input file list is an URL to an OWL/OBO ontology.

        For each URL, the referenced ontology is downloaded, and used as input to an OWLTools command line argument (

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Function normalizes_source_codes has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.

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def normalizes_source_codes(data: pd.DataFrame, source_code_dict: Dict) -> pd.Series:
    """Takes a Pandas DataFrame column containing source code values that need normalization and normalizes them
    using values from a pre-built dictionary (resources/mappings/source_code_vocab_map.csv). The function is designed
    to normalize identifier prefixes according to the specifications in the source_code_dict. It provides some light
    regex support for the following scenarios:

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Function filters_mapping_content has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

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def filters_mapping_content(exact_results: List, similarity_results: List, threshold: float) -> Tuple:
    """Parses compiled mapping results, when results exist, to determine a final aggregated mapping result.

    Args:
        exact_results: A nested list containing 3 sub-lists where sub-list[0] contains exact match uris, sub-list[1]

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Function creates_concept_set_container has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

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def creates_concept_set_container(map_dict: Dict, output_loc: str, enclave_params: Dict) -> None:
    """Takes input information on the OMOP2OBO mappings and outputs a csv file with the columns required for creating
    the concept set container data.

    Args:

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Function parses_resource_file has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

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    def parses_resource_file(self) -> None:
        """Parses data from a file and outputs a list where each item is a line from the input text file.

        Returns:
            source_list: A dictionary, where the key is the type of data and the value is the file path or url. See

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Function creates_concept_set_version has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

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def creates_concept_set_version(map_dict: Dict, id_dict: Dict, output_loc: str, enclave_params: Dict) -> None:
    """Takes input information on the OMOP2OBO mappings and outputs a csv file with the columns required for creating
    the concept set version data.

    Args:

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Function creates_concept_set_expression_items has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.

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def creates_concept_set_expression_items(map_dict: Dict, id_dict: Dict, output_loc: str, enclave_params: Dict) -> None:
    """Takes input information on the OMOP2OBO mappings and outputs a csv file with the columns required for creating
    the concept set expression items data.

    Args:

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