Module phc.easy.summary.options.item_counts

Expand source code
from enum import Enum
from typing import Union

from phc.easy.summary.options.clinical_counts import (
    SummaryClinicalCountsOptions,
)


class SummaryClinicalType(str, Enum):
    OBSERVATION = "observation"
    CONDITION = "condition"
    MEDICATION = "medication"
    PROCEDURE = "procedure"
    MEDIA = "media"
    DEMOGRAPHIC = "demographic"

    # NOTE: Patient is not included because it's just a count
    # PATIENT = "patient"

    @classmethod
    def has_value(cls, value):
        return any(value == item.value for item in cls)


class SummaryOmicsType(str, Enum):
    TEST = "test"
    SEQUENCE = "sequence"
    GENE_VARIANT = "gene-variant"
    COPY_NUMBER_STATUS = "copynumber-status"
    CLINVAR_SIG = "clinvar-significance"
    ONCOPRINT = "oncoprint"

    @classmethod
    def has_value(cls, value):
        return any(value == item.value for item in cls)


class SummaryItemCountsOptions(SummaryClinicalCountsOptions):
    summary: Union[SummaryClinicalType, SummaryOmicsType]

Classes

class SummaryClinicalType (value, names=None, *, module=None, qualname=None, type=None, start=1)

An enumeration.

Expand source code
class SummaryClinicalType(str, Enum):
    OBSERVATION = "observation"
    CONDITION = "condition"
    MEDICATION = "medication"
    PROCEDURE = "procedure"
    MEDIA = "media"
    DEMOGRAPHIC = "demographic"

    # NOTE: Patient is not included because it's just a count
    # PATIENT = "patient"

    @classmethod
    def has_value(cls, value):
        return any(value == item.value for item in cls)

Ancestors

  • builtins.str
  • enum.Enum

Class variables

var CONDITION
var DEMOGRAPHIC
var MEDIA
var MEDICATION
var OBSERVATION
var PROCEDURE

Static methods

def has_value(value)
Expand source code
@classmethod
def has_value(cls, value):
    return any(value == item.value for item in cls)
class SummaryItemCountsOptions (**data: Any)

Create a new model by parsing and validating input data from keyword arguments.

Raises ValidationError if the input data cannot be parsed to form a valid model.

Expand source code
class SummaryItemCountsOptions(SummaryClinicalCountsOptions):
    summary: Union[SummaryClinicalType, SummaryOmicsType]

Ancestors

Class variables

var summary : Union[SummaryOmicsTypeSummaryClinicalType]

Methods

def dict(self)

Inherited from: SummaryClinicalCountsOptions.dict

Generate a dictionary representation of the model, optionally specifying which fields to include or exclude.

class SummaryOmicsType (value, names=None, *, module=None, qualname=None, type=None, start=1)

An enumeration.

Expand source code
class SummaryOmicsType(str, Enum):
    TEST = "test"
    SEQUENCE = "sequence"
    GENE_VARIANT = "gene-variant"
    COPY_NUMBER_STATUS = "copynumber-status"
    CLINVAR_SIG = "clinvar-significance"
    ONCOPRINT = "oncoprint"

    @classmethod
    def has_value(cls, value):
        return any(value == item.value for item in cls)

Ancestors

  • builtins.str
  • enum.Enum

Class variables

var CLINVAR_SIG
var COPY_NUMBER_STATUS
var GENE_VARIANT
var ONCOPRINT
var SEQUENCE
var TEST

Static methods

def has_value(value)
Expand source code
@classmethod
def has_value(cls, value):
    return any(value == item.value for item in cls)