Module `phc.easy.omics.options.genomic_structural_variant`

Expand source code

from typing import List, Optional
from pydantic import Field
from phc.easy.abstract.paging_api_item import PagingApiOptions
from phc.easy.omics.options.common import GenomicVariantInclude
from phc.easy.omics.options.structural_type import StructuralType
from phc.easy.omics.options.in_frame import InFrame

MAPPINGS = {
    "variant_set_ids": "structuralVariantSetIds",
    "effect": "type",
    "in_frame": "inFrame",
    "in_ckb": "drugAssociations",
}


class GenomicStructuralVariantOptions(PagingApiOptions):
    variant_set_ids: List[str] = Field(..., min_items=1)
    gene: List[str] = []
    effect: List[StructuralType] = []
    interpretation: List[str] = []
    in_frame: List[InFrame] = []
    in_ckb: Optional[bool] = None
    include: List[GenomicVariantInclude] = []

    @staticmethod
    def transform(key, value):
        if isinstance(value, list):
            value = ",".join(
                [elem if isinstance(elem, str) else str(elem) for elem in value]
            )
        elif isinstance(value, bool):
            value = "true" if value else None

        return (MAPPINGS.get(key, key), value)

Classes

class GenomicStructuralVariantOptions (**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 GenomicStructuralVariantOptions(PagingApiOptions):
    variant_set_ids: List[str] = Field(..., min_items=1)
    gene: List[str] = []
    effect: List[StructuralType] = []
    interpretation: List[str] = []
    in_frame: List[InFrame] = []
    in_ckb: Optional[bool] = None
    include: List[GenomicVariantInclude] = []

    @staticmethod
    def transform(key, value):
        if isinstance(value, list):
            value = ",".join(
                [elem if isinstance(elem, str) else str(elem) for elem in value]
            )
        elif isinstance(value, bool):
            value = "true" if value else None

        return (MAPPINGS.get(key, key), value)

Ancestors

PagingApiOptions
pydantic.main.BaseModel
pydantic.utils.Representation

Class variables

var effect : List[StructuralType]
var gene : List[str]
var in_ckb : Optional[bool]
var in_frame : List[InFrame]
var include : List[GenomicVariantInclude]
var interpretation : List[str]
var variant_set_ids : List[str]

Static methods

def transform(key, value)

Expand source code

@staticmethod
def transform(key, value):
    if isinstance(value, list):
        value = ",".join(
            [elem if isinstance(elem, str) else str(elem) for elem in value]
        )
    elif isinstance(value, bool):
        value = "true" if value else None

    return (MAPPINGS.get(key, key), value)

Methods

def dict(self): Inherited from: PagingApiOptions.dict

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