kb_python.validate
¶
Module Contents¶
Functions¶
validate_bus (path) |
Verify if the provided BUS file is valid. |
validate_mtx (path) |
Verify if the provided Matrix Market (.mtx) file is valid. |
validate (path) |
Validate a file. |
validate_files (pre=True, post=True) |
Function decorator to validate input/output files. |
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kb_python.validate.
logger
¶
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kb_python.validate.
BUSTOOLS_INSPECT_PARSER
¶
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exception
kb_python.validate.
FileVerificationFailed
¶ Bases:
Exception
Common base class for all non-exit exceptions.
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kb_python.validate.
validate_bus
(path)¶ 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 (str) – path to BUS file
Raises: - FileVerificationFailed – if the file failed verification
- subprocess.CalledProcessError – if the bustools command failed
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kb_python.validate.
validate_mtx
(path)¶ 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 (str) – path to mtx file Raises: FileVerificationFailed – if the file failed verification
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kb_python.validate.
VALIDATORS
¶
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kb_python.validate.
validate
(path)¶ 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 (str) – path to file Raises: FileVerificationFailed – if the file failed verification
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kb_python.validate.
validate_files
(pre=True, post=True)¶ Function decorator to validate input/output files.
This function does not validate when the current run is a dry run.
Parameters: - pre (bool) – whether to validate input files, defaults to True
- post (bool) – whether to validate output files, defaults to True
Returns: wrapped function
Return type: function