File fhir_server.py has 862 lines of code (exceeds 250 allowed). Consider refactoring.

Open

import os
import re
from typing import Iterable, List, Union

import fhir.resources

File dataset.py has 457 lines of code (exceeds 250 allowed). Consider refactoring.

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import random
from typing import Dict, List, Optional, Type, Union
from uuid import uuid4

import matplotlib.pyplot as plt

FhirServer has 31 functions (exceeds 20 allowed). Consider refactoring.

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class FhirServer:
    def __init__(
        self,
        api_address: str,
        username: Union[str, None] = None,

File base.py has 310 lines of code (exceeds 250 allowed). Consider refactoring.

Open

from inspect import signature
from typing import Any, Callable, List, TypeVar, Union

import fhir.resources
import httpx

Function _resolve_xml_pagination has a Cognitive Complexity of 23 (exceeds 5 allowed). Consider refactoring.

Open

    def _resolve_xml_pagination(self, server_response: httpx.Response) -> str:
        # parse the xml response and extract the initial entries
        initial_response = xmltodict.parse(server_response.text)
        entries = initial_response["Bundle"].get("entry")

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File bench.py has 300 lines of code (exceeds 250 allowed). Consider refactoring.

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import os
import time
from datetime import datetime
from typing import Any, List, Tuple, Union

Function __repr__ has a Cognitive Complexity of 20 (exceeds 5 allowed). Consider refactoring.

Open

    def __repr__(self):
        resource = self.resource.resource_type
        if self.query_parameters.include_parameters:
            includes = []
            rev_includes = []

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File query_parameters.py has 281 lines of code (exceeds 250 allowed). Consider refactoring.

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from abc import ABC
from enum import Enum
from typing import List, Optional, Tuple, Union

from pydantic import BaseModel, root_validator, validator

Function _resolve_json_pagination has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.

Open

    def _resolve_json_pagination(
        self,
        initial_response: httpx.Response,
        page_callback: Union[
            Callable[[List[FHIRAbstractModel]], Any], Callable[[], Any], None

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Function _setup has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.

Open

    def _setup(
        self,
        queries: Union[List[Tuple[str, Union[str, FhirQueryParameters]]], None] = None,
        steps: List[Union[str, BenchmarkOperations]] = None,
    ):

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Function __init__ has 19 arguments (exceeds 4 allowed). Consider refactoring.

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    def __init__(

Function _get_required_reference has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.

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    def _get_required_reference(
        resource: Union[FHIRResourceModel, Type[FHIRAbstractModel]]
    ) -> str:
        fields = get_resource_fields(resource)
        required_fields = []

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Function extract_references has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.

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def extract_references(resource: Resource) -> List[Tuple[str, str, str, bool]]:
    """
    Extracts the references from a resource and returns them as a list of dicts.
    Args:
        resource: fhir resource object to extract references from.

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Function flatten_dict has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.

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def flatten_dict(
    d, parent_key: str = "", sep: str = "_", keys: List[str] = None
) -> dict:
    """
    Flatten a nested dictionary into a single level dictionary.

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DatasetGenerator has 21 functions (exceeds 20 allowed). Consider refactoring.

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class DatasetGenerator:

    """
    Generates a dataset of FHIR resources.
    """

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

Open

def make_transaction_entry(
    method: Union[TransactionMethod, str],
    url: str = None,
    resource: Union[Resource, dict] = None,
) -> BundleEntry:

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

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    def generate(
        self,
        references: bool = False,
        generate_ids: bool = False,
        as_dict: bool = False,

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Function include has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.

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    def include(
        self: T,
        resource: str = None,
        reference_param: str = None,
        target: str = None,

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Function _validate_depends has a Cognitive Complexity of 14 (exceeds 5 allowed). Consider refactoring.

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    def _validate_depends(
        self,
        depends_on: Union[str, List[str]],
    ):
        graph = self.graph()

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Function _get_refs_for_generator has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring.

Open

    def _get_refs_for_generator(
        self, generator: DataSetResourceGenerator, result: dict
    ) -> dict:
        """Get the references resources for a generator from the results and insert a reference to them into
        the reference field of the generator

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