Module `phc.easy.option`

Expand source code

from phc.easy.ocr.options.ocr_config_types import Config as OcrConfig
from phc.easy.omics.options.chromosome import Chromosome
from phc.easy.omics.options.clinvar_review import ClinVarReview
from phc.easy.omics.options.clinvar_significance import ClinVarSignificance
from phc.easy.omics.options.coding_effect import CodingEffect
from phc.easy.omics.options.common import GenomicVariantInclude
from phc.easy.omics.options.copy_number_status import CopyNumberStatus
from phc.easy.omics.options.gene_class import GeneClass
from phc.easy.omics.options.genomic_copy_number_variant import (
    GenomicCopyNumberVariantOptions,
)
from phc.easy.omics.options.genomic_short_variant import (
    GenomicShortVariantOptions,
)
from phc.easy.omics.options.genomic_test import (
    GenomicTestStatus,
    GenomicTestType,
)
from phc.easy.omics.options.in_frame import InFrame
from phc.easy.omics.options.structural_type import StructuralType
from phc.easy.omics.options.zygosity import Zygosity
from phc.easy.summary.options.clinical_counts import (
    SummaryClinicalCountsOptions,
)
from phc.easy.summary.options.item_counts import (
    SummaryClinicalType,
    SummaryItemCountsOptions,
    SummaryOmicsType,
)


class Option:
    """Class that references all available API options"""

    # Omics
    GenomicVariantInclude = GenomicVariantInclude
    GenomicCopyNumberVariantOptions = GenomicCopyNumberVariantOptions
    GenomicShortVariantOptions = GenomicShortVariantOptions
    GenomicTestType = GenomicTestType
    GenomicTestStatus = GenomicTestStatus
    CodingEffect = CodingEffect
    Chromosome = Chromosome
    ClinVarSignificance = ClinVarSignificance
    ClinVarReview = ClinVarReview
    GeneClass = GeneClass
    Zygosity = Zygosity
    CopyNumberStatus = CopyNumberStatus
    InFrame = InFrame
    StructuralType = StructuralType

    # OCR
    OcrConfig = OcrConfig

    # Summary APIs
    SummaryItemCountsOptions = SummaryItemCountsOptions
    SummaryOmicsType = SummaryOmicsType
    SummaryClinicalType = SummaryClinicalType
    SummaryClinicalCountsOptions = SummaryClinicalCountsOptions

Classes

class Option

Class that references all available API options

Expand source code

class Option:
    """Class that references all available API options"""

    # Omics
    GenomicVariantInclude = GenomicVariantInclude
    GenomicCopyNumberVariantOptions = GenomicCopyNumberVariantOptions
    GenomicShortVariantOptions = GenomicShortVariantOptions
    GenomicTestType = GenomicTestType
    GenomicTestStatus = GenomicTestStatus
    CodingEffect = CodingEffect
    Chromosome = Chromosome
    ClinVarSignificance = ClinVarSignificance
    ClinVarReview = ClinVarReview
    GeneClass = GeneClass
    Zygosity = Zygosity
    CopyNumberStatus = CopyNumberStatus
    InFrame = InFrame
    StructuralType = StructuralType

    # OCR
    OcrConfig = OcrConfig

    # Summary APIs
    SummaryItemCountsOptions = SummaryItemCountsOptions
    SummaryOmicsType = SummaryOmicsType
    SummaryClinicalType = SummaryClinicalType
    SummaryClinicalCountsOptions = SummaryClinicalCountsOptions

Class variables

var Chromosome

An enumeration.

var ClinVarReview

An enumeration.

var ClinVarSignificance

An enumeration.

var CodingEffect

An enumeration.

var CopyNumberStatus

An enumeration.

var GeneClass

An enumeration.

var GenomicCopyNumberVariantOptions

Options to pass to /v1/genomics/copy-numbers

var GenomicShortVariantOptions

Options to pass to /v1/genomics/variants

var GenomicTestStatus

An enumeration.

var GenomicTestType

An enumeration.

var GenomicVariantInclude

An enumeration.

var InFrame

An enumeration.

var OcrConfig

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.

var StructuralType

An enumeration.

var SummaryClinicalCountsOptions

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.

var SummaryClinicalType

An enumeration.

var SummaryItemCountsOptions

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.

var SummaryOmicsType

An enumeration.

var Zygosity

An enumeration.