Module phc.easy.omics.options.genomic_expression

Classes

class EXPRESSION (...)

str(object='') -> str str(bytes_or_buffer[, encoding[, errors]]) -> str

Create a new string object from the given object. If encoding or errors is specified, then the object must expose a data buffer that will be decoded using the given encoding and error handler. Otherwise, returns the result of object.str() (if defined) or repr(object). encoding defaults to sys.getdefaultencoding(). errors defaults to 'strict'.

Ancestors

• pydantic.types.ConstrainedStr
• builtins.str

Class variables

var curtail_length

var max_length

var min_length

var regex

var strict

var strip_whitespace

var to_lower

var to_upper

class ORDER_BY (...)

str(object='') -> str str(bytes_or_buffer[, encoding[, errors]]) -> str

Create a new string object from the given object. If encoding or errors is specified, then the object must expose a data buffer that will be decoded using the given encoding and error handler. Otherwise, returns the result of object.str() (if defined) or repr(object). encoding defaults to sys.getdefaultencoding(). errors defaults to 'strict'.

Ancestors

• pydantic.types.ConstrainedStr
• builtins.str

Class variables

var curtail_length

var max_length

var min_length

var regex

var strict

var strip_whitespace

var to_lower

var to_upper

class GenomicExpressionOptions (**data: Any)

Options to pass to /v1/genomics/expressions

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 GenomicExpressionOptions(PagingApiOptions):
    """Options to pass to `/v1/genomics/expressions`"""

    variant_set_ids: List[str] = Field(..., min_items=1)
    include: List[GenomicVariantInclude] = []
    gene: List[str] = []
    expression: Optional[EXPRESSION] = None
    order_by: Optional[ORDER_BY] = None
    in_ckb: Optional[bool] = None
    # TODO: Fill out allowed options for this parameter
    outlier_std_dev: Optional[str] = None

    @staticmethod
    def transform(key, value):
        if key == "expression" and value is not None:
            value = GenomicExpressionOptions.transform_expression(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)

    @staticmethod
    def transform_expression(value: str):
        value = value.replace(" ", "")

        if ">=" in value:
            return value.replace(">=", "") + ":gte"

        if "<=" in value:
            return value.replace("<=", "") + ":lte"

        return value

Ancestors

• PagingApiOptions
• pydantic.main.BaseModel
• pydantic.utils.Representation

Class variables

var expression : Optional[ConstrainedStrValue]

var gene : List[str]

var in_ckb : Optional[bool]

var include : List[GenomicVariantInclude]

var order_by : Optional[ConstrainedStrValue]

var outlier_std_dev : Optional[str]

var variant_set_ids : List[str]

Static methods

def transform(key, value)

Expand source code

@staticmethod
def transform(key, value):
    if key == "expression" and value is not None:
        value = GenomicExpressionOptions.transform_expression(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)

def transform_expression(value: str)

Expand source code

@staticmethod
def transform_expression(value: str):
    value = value.replace(" ", "")

    if ">=" in value:
        return value.replace(">=", "") + ":gte"

    if "<=" in value:
        return value.replace("<=", "") + ":lte"

    return value

Methods

def dict(self)

Inherited from: PagingApiOptions.dict

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