Fileformat

genie.example_filetype_format

TODO: Rename this to model.py This contains the GENIE model objects

Attributes

logger = logging.getLogger(__name__) module-attribute

Classes

ValidationResults dataclass

Validation results

Functions

is_valid()

True if file is valid

collect_errors_and_warnings()

Aggregates error and warnings into a string.

RETURNS	DESCRIPTION
str	A message containing errors and warnings. TYPE: str

FileTypeFormat

Functions

__init__(syn, center, genie_config=None, ancillary_files=None)

A validator helper class for a center's files.

PARAMETER	DESCRIPTION
syn	a synapseclient.Synapse object TYPE: Synapse
center	The participating center name. TYPE: str
genie_config	The configurations needed for the GENIE codebase. GENIE table type/name to Synapse Id. Defaults to None. TYPE: dict DEFAULT: None
ancillary_files	all files downloaded for validation. Defaults to None. TYPE: List[List[Entity]] DEFAULT: None

read_file(filePathList)

Each file is to be read in for validation and processing. This is not to be changed in any functions.

PARAMETER	DESCRIPTION
filePathList	A list of file paths (Max is 2 for the two clinical files)

RETURNS	DESCRIPTION
df	Pandas dataframe of file

validateFilename(filePath)

Validation of file name. The filename is what maps the file to its validation and processing.

PARAMETER	DESCRIPTION
filePath	Path to file

RETURNS	DESCRIPTION
str	file type defined by self._fileType

process_steps(df, **kwargs)

This function is modified for every single file. It reformats the file and stores the file into database and Synapse.

preprocess(newpath)

This is for any preprocessing that has to occur to the entity name to add to kwargs for processing. entity name is included in the new path

PARAMETER	DESCRIPTION
newpath	Path to file

process(filePath, **kwargs)

This is the main processing function.

PARAMETER	DESCRIPTION
filePath	Path to file
kwargs	The kwargs are determined by self._process_kwargs DEFAULT: {}

RETURNS	DESCRIPTION
str	file path of processed file

validate(filePathList, **kwargs)

This is the main validation function. Every file type calls self._validate, which is different.

PARAMETER	DESCRIPTION
filePathList	A list of file paths.
kwargs	The kwargs are determined by self._validation_kwargs DEFAULT: {}

RETURNS	DESCRIPTION
tuple	The errors and warnings as a file from validation. TYPE: ValidationResults