kb_python.validate

Module Contents

Functions

validate_bus(path: str)

Verify if the provided BUS file is valid.

validate_mtx(path: str)

Verify if the provided Matrix Market (.mtx) file is valid.

validate(path: str)

Validate a file.

validate_files(pre: bool = True, post: bool = True) → Callable

Function decorator to validate input/output files.

Attributes

BUSTOOLS_INSPECT_PARSER

VALIDATORS

kb_python.validate.BUSTOOLS_INSPECT_PARSER
exception kb_python.validate.ValidateError

Bases: Exception

Common base class for all non-exit exceptions.

kb_python.validate.validate_bus(path: str)

Verify if the provided BUS file is valid.

A BUS file is considered valid when bustools inspect can read the file + it has > 0 BUS records.

Parameters

path – Path to BUS file

Raises
  • ValidateError – If the file failed verification

  • subprocess.CalledProcessError – If the bustools command failed

kb_python.validate.validate_mtx(path: str)

Verify if the provided Matrix Market (.mtx) file is valid.

A BUS file is considered valid when the file can be read with scipy.io.mmread.

Parameters

path – Path to mtx file

Raises

ValidateError – If the file failed verification

kb_python.validate.VALIDATORS
kb_python.validate.validate(path: str)

Validate a file.

This function is a wrapper around all validation functions. Given a path, it chooses the correct validation function. This function assumes the file exists.

Parameters

path – Path to file

Raises

ValidateError – If the file failed verification

kb_python.validate.validate_files(pre: bool = True, post: bool = True) Callable

Function decorator to validate input/output files.

This function does not validate when the current run is a dry run. The decorated function is expected to return a dictionary of paths as values.

Parameters
  • pre – Whether to validate input files, defaults to True

  • post – Whether to validate output files, defaults to True

Returns

Wrapped function