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)

Usage docs: https://docs.pydantic.dev/2.10/concepts/models/

A base class for creating Pydantic models.

Attributes

__class_vars__: The names of the class variables defined on the model.
__private_attributes__: Metadata about the private attributes of the model.
__signature__: The synthesized __init__ [Signature][inspect.Signature] of the model.
__pydantic_complete__: Whether model building is completed, or if there are still undefined fields.
__pydantic_core_schema__: The core schema of the model.
__pydantic_custom_init__: Whether the model has a custom __init__ function.
__pydantic_decorators__: Metadata containing the decorators defined on the model. This replaces Model.__validators__ and Model.__root_validators__ from Pydantic V1.
__pydantic_generic_metadata__: Metadata for generic models; contains data used for a similar purpose to args, origin, parameters in typing-module generics. May eventually be replaced by these.
__pydantic_parent_namespace__: Parent namespace of the model, used for automatic rebuilding of models.
__pydantic_post_init__: The name of the post-init method for the model, if defined.
__pydantic_root_model__: Whether the model is a [RootModel][pydantic.root_model.RootModel].
__pydantic_serializer__: The pydantic-core SchemaSerializer used to dump instances of the model.
__pydantic_validator__: The pydantic-core SchemaValidator used to validate instances of the model.
__pydantic_fields__: A dictionary of field names and their corresponding [FieldInfo][pydantic.fields.FieldInfo] objects.
__pydantic_computed_fields__: A dictionary of computed field names and their corresponding [ComputedFieldInfo][pydantic.fields.ComputedFieldInfo] objects.
__pydantic_extra__: A dictionary containing extra values, if [extra][pydantic.config.ConfigDict.extra] is set to 'allow'.
__pydantic_fields_set__: The names of fields explicitly set during instantiation.
__pydantic_private__: Values of private attributes set on the model instance.

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

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

Expand source code

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

Ancestors

Class variables

var model_config
var summary : Union[SummaryOmicsType, SummaryClinicalType]

Methods

def model_dump(self): Inherited from: SummaryClinicalCountsOptions.model_dump

Usage docs: https://docs.pydantic.dev/2.10/concepts/serialization/#modelmodel_dump …

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)