Module `phc.easy.sequence`

Expand source code

import pandas as pd

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


class Sequence(FhirServicePatientItem):
    @staticmethod
    def table_name():
        return "sequence"

    @staticmethod
    def patient_key() -> str:
        return "patient.reference"

    @staticmethod
    def transform_results(data_frame: pd.DataFrame, **expand_args):
        args = {
            **expand_args,
            "code_columns": [
                *expand_args.get("code_columns", []),
                "specimen",
                "repository",
            ],
            "custom_columns": [
                *expand_args.get("custom_columns", []),
                Frame.codeable_like_column_expander("patient"),
                Frame.codeable_like_column_expander("referenceSeq"),
            ],
        }

        return Frame.expand(data_frame, **args)

Classes

class Sequence

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

Expand source code

class Sequence(FhirServicePatientItem):
    @staticmethod
    def table_name():
        return "sequence"

    @staticmethod
    def patient_key() -> str:
        return "patient.reference"

    @staticmethod
    def transform_results(data_frame: pd.DataFrame, **expand_args):
        args = {
            **expand_args,
            "code_columns": [
                *expand_args.get("code_columns", []),
                "specimen",
                "repository",
            ],
            "custom_columns": [
                *expand_args.get("custom_columns", []),
                Frame.codeable_like_column_expander("patient"),
                Frame.codeable_like_column_expander("referenceSeq"),
            ],
        }

        return Frame.expand(data_frame, **args)

Ancestors

Static methods

def code_fields() ‑> List[str]

Inherited from: FhirServicePatientItem.code_fields

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

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() ‑> str

Expand source code

@staticmethod
def patient_key() -> str:
    return "patient.reference"

def table_name()

Inherited from: FhirServicePatientItem.table_name

Returns the FSS table name for retrieval

Expand source code

@staticmethod
def table_name():
    return "sequence"

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

Inherited from: FhirServicePatientItem.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", []),
            "specimen",
            "repository",
        ],
        "custom_columns": [
            *expand_args.get("custom_columns", []),
            Frame.codeable_like_column_expander("patient"),
            Frame.codeable_like_column_expander("referenceSeq"),
        ],
    }

    return Frame.expand(data_frame, **args)