Module `phc.easy.patients`

Expand source code

import pandas as pd

from phc.easy.frame import Frame
from phc.easy.abstract.fhir_service_item import FhirServiceItem
from phc.easy.patients.address import expand_address_column
from phc.easy.patients.name import expand_name_column


class Patient(FhirServiceItem):
    @staticmethod
    def table_name():
        return "patient"

    @staticmethod
    def code_fields():
        return [
            "extension.valueCodeableConcept.coding",
            "identifier.type.coding",
            "maritalStatus.coding",
            "meta.tag",
        ]

    @staticmethod
    def transform_results(data_frame: pd.DataFrame, **expand_args):
        args = {
            **expand_args,
            "code_columns": [
                *expand_args.get("code_columns", []),
                "contained",
                "maritalStatus",
            ],
            "custom_columns": [
                *expand_args.get("custom_columns", []),
                Frame.codeable_like_column_expander("managingOrganization"),
                ("address", expand_address_column),
                ("name", expand_name_column),
            ],
        }

        return Frame.expand(data_frame, **args)

Sub-modules

phc.easy.patients.address
phc.easy.patients.name

Classes

class Patient

Provides an abstract class and/or static methods for retrieving items from a FSS table

Expand source code

class Patient(FhirServiceItem):
    @staticmethod
    def table_name():
        return "patient"

    @staticmethod
    def code_fields():
        return [
            "extension.valueCodeableConcept.coding",
            "identifier.type.coding",
            "maritalStatus.coding",
            "meta.tag",
        ]

    @staticmethod
    def transform_results(data_frame: pd.DataFrame, **expand_args):
        args = {
            **expand_args,
            "code_columns": [
                *expand_args.get("code_columns", []),
                "contained",
                "maritalStatus",
            ],
            "custom_columns": [
                *expand_args.get("custom_columns", []),
                Frame.codeable_like_column_expander("managingOrganization"),
                ("address", expand_address_column),
                ("name", expand_name_column),
            ],
        }

        return Frame.expand(data_frame, **args)

Ancestors

FhirServiceItem

Static methods

def code_fields()

Inherited from: FhirServiceItem.code_fields

Returns the code keys (e.g. when searching for codes)

Expand source code

@staticmethod
def code_fields():
    return [
        "extension.valueCodeableConcept.coding",
        "identifier.type.coding",
        "maritalStatus.coding",
        "meta.tag",
    ]

def get_codes(display_query: Optional[str] = None, sample_size: Optional[int] = None, exclude_meta_tag=True, **kwargs)

Inherited from: FhirServiceItem.get_codes

Find all codes …

def get_count(query_overrides: dict = {}, auth_args=<phc.easy.auth.Auth object>)

Inherited from: FhirServiceItem.get_count

Get the count for a given FSS query

def get_count_by_field(field: str, **kwargs)

Inherited from: FhirServiceItem.get_count_by_field

Count records by a given field …

def get_data_frame(all_results: bool = False, raw: bool = False, page_size: Optional[int] = None, max_pages: Optional[int] = None, query_overrides: dict = {}, auth_args=<phc.easy.auth.Auth object>, ignore_cache: bool = False, expand_args: dict = {}, log: bool = False, id: Optional[str] = None, ids: List[str] = [], term: Optional[dict] = None, terms: List[dict] = [], max_terms: int = 30000, code: Union[str, List[str], None] = None, display: Union[str, List[str], None] = None, system: Union[str, List[str], None] = None, code_fields: List[str] = [])

Inherited from: FhirServiceItem.get_data_frame

Retrieve records …

def table_name()

Inherited from: FhirServiceItem.table_name

Returns the FSS table name for retrieval

Expand source code

@staticmethod
def table_name():
    return "patient"

def transform_results(data_frame: pandas.core.frame.DataFrame, **expand_args)

Inherited from: FhirServiceItem.transform_results

Transform data frame batch

Expand source code

@staticmethod
def transform_results(data_frame: pd.DataFrame, **expand_args):
    args = {
        **expand_args,
        "code_columns": [
            *expand_args.get("code_columns", []),
            "contained",
            "maritalStatus",
        ],
        "custom_columns": [
            *expand_args.get("custom_columns", []),
            Frame.codeable_like_column_expander("managingOrganization"),
            ("address", expand_address_column),
            ("name", expand_name_column),
        ],
    }

    return Frame.expand(data_frame, **args)