Module `phc.easy.provenance`

Expand source code

import pandas as pd

from phc.easy.frame import Frame
from phc.easy.abstract.fhir_service_patient_item import FhirServicePatientItem


class Provenance(FhirServicePatientItem):
    @staticmethod
    def table_name():
        return "provenance"

    @staticmethod
    def patient_key():
        """Patient relationship is based on who signed this provenance"""
        return "signature.whoReference.reference"

    @staticmethod
    def code_fields():
        return ["signature.type", "agent.role.coding", "meta.tag"]

    @staticmethod
    def transform_results(df: pd.DataFrame, **expand_args):
        return Frame.expand(
            df,
            date_columns=[
                *expand_args.get("date_columns", []),
                "recorded",
                "signature.when",
            ],
            code_columns=[
                *expand_args.get("code_columns", []),
                "agent",
                "signature",
            ],
        )

Classes

class Provenance

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

Expand source code

class Provenance(FhirServicePatientItem):
    @staticmethod
    def table_name():
        return "provenance"

    @staticmethod
    def patient_key():
        """Patient relationship is based on who signed this provenance"""
        return "signature.whoReference.reference"

    @staticmethod
    def code_fields():
        return ["signature.type", "agent.role.coding", "meta.tag"]

    @staticmethod
    def transform_results(df: pd.DataFrame, **expand_args):
        return Frame.expand(
            df,
            date_columns=[
                *expand_args.get("date_columns", []),
                "recorded",
                "signature.when",
            ],
            code_columns=[
                *expand_args.get("code_columns", []),
                "agent",
                "signature",
            ],
        )

Ancestors

Static methods

def code_fields()

Inherited from: FhirServicePatientItem.code_fields

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

Expand source code

@staticmethod
def code_fields():
    return ["signature.type", "agent.role.coding", "meta.tag"]

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

Inherited from: FhirServicePatientItem.get_codes

Find all codes …

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

Inherited from: FhirServicePatientItem.get_count

Get the count for a given FSS query

def get_count_by_field(field: str, **kwargs)

Inherited from: FhirServicePatientItem.get_count_by_field

Count records by a given field …

def get_count_by_patient(**kwargs)

Inherited from: FhirServicePatientItem.get_count_by_patient

Count records by a given field …

def get_data_frame(all_results: bool = False, raw: bool = False, id: Optional[str] = None, ids: List[str] = [], patient_id: Optional[str] = None, patient_ids: List[str] = [], device_id: Optional[str] = None, device_ids: List[str] = [], 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, 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: FhirServicePatientItem.get_data_frame

Retrieve records …

def patient_key()

Patient relationship is based on who signed this provenance

Expand source code

@staticmethod
def patient_key():
    """Patient relationship is based on who signed this provenance"""
    return "signature.whoReference.reference"

def table_name()

Inherited from: FhirServicePatientItem.table_name

Returns the FSS table name for retrieval

Expand source code

@staticmethod
def table_name():
    return "provenance"

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

Inherited from: FhirServicePatientItem.transform_results

Transform data frame batch

Expand source code

@staticmethod
def transform_results(df: pd.DataFrame, **expand_args):
    return Frame.expand(
        df,
        date_columns=[
            *expand_args.get("date_columns", []),
            "recorded",
            "signature.when",
        ],
        code_columns=[
            *expand_args.get("code_columns", []),
            "agent",
            "signature",
        ],
    )