"""Validation class for BIDS projects."""
import logging
import os
import re
from functools import lru_cache
from itertools import chain
import bidsschematools as bst
import bidsschematools.rules
import bidsschematools.schema
import bidsschematools.utils
import bidsschematools.validator
class LoggingContext:
# From logging cookbook (CC0):
# https://docs.python.org/3/howto/logging-cookbook.html#using-a-context-manager-for-selective-logging
#
# Changes:
# - Added docstrings (2024.05.06)
"""Context manager to temporarily modify logging configuration.
Parameters
----------
logger : logging.Logger
Logger object to be modified.
level : int
Logging level to set temporarily. If None, the level is not
modified.
handler : logging.Handler
Handler to add temporarily. If None, no handler is added.
close : bool
Whether to close the handler after removing it. Defaults to True.
"""
def __init__(self, logger, level=None, handler=None, close=True):
self.logger = logger
self.level = level
self.handler = handler
self.close = close
def __enter__(self):
if self.level is not None:
self.old_level = self.logger.level
self.logger.setLevel(self.level)
if self.handler:
self.logger.addHandler(self.handler)
def __exit__(self, et, ev, tb):
if self.level is not None:
self.logger.setLevel(self.old_level)
if self.handler:
self.logger.removeHandler(self.handler)
if self.handler and self.close:
self.handler.close()
[docs]
class BIDSValidator:
"""Object for BIDS (Brain Imaging Data Structure) verification.
The main method of this class is `is_bids()`. You should use it for
checking whether a file path is compatible with BIDS.
"""
regexes = None
[docs]
def __init__(self, index_associated=True):
"""Initialize BIDSValidator object.
Parameters
----------
index_associated : bool
Specifies if an associated data should be checked. If it is true
then any file paths in directories `code/`, `derivatives/`,
`sourcedata/` and `stimuli/` will pass the validation, else they
won't. Defaults to True.
"""
self.index_associated = index_associated
@classmethod
def _init_regexes(cls):
if cls.regexes is None:
with LoggingContext(bst.utils.get_logger(), level=logging.WARNING):
schema = bst.schema.load_schema()
all_rules = chain.from_iterable(
bst.rules.regexify_filename_rules(group, schema, level=2)
for group in (schema.rules.files.common, schema.rules.files.raw)
)
cls.regexes = [rule['regex'] for rule in all_rules]
@classmethod
def parse(cls, path):
"""Parse a file path into a dictionary of BIDS entities.
Parameters
----------
path : str
Path of a file to be parsed. Must be relative to root of a BIDS
dataset, and must include a leading forward slash `/`.
Returns
-------
dict
Dictionary of BIDS entities. Keys are entity names, values are
entity values. If the file path is not compatible with BIDS, an
empty dictionary is returned.
Notes
-----
When you test a file path, make sure that the path is relative to the
root of the BIDS dataset the file is part of. That is, as soon as the
file path contains parts outside of the BIDS dataset, the validation
will fail. For example "home/username/my_dataset/participants.tsv" will
fail, although "/participants.tsv" is a valid BIDS file.
Examples
--------
>>> from bids_validator import BIDSValidator
>>> validator = BIDSValidator()
>>> validator.parse("/sub-01/anat/sub-01_rec-CSD_T1w.nii.gz")
{'subject': '01', 'datatype': 'anat', 'reconstruction': 'CSD', 'suffix': 'T1w',
'extension': '.nii.gz'}
>>> validator.parse("/sub-01/anat/sub-01_acq-23_rec-CSD_T1w.exe")
{}
>>> validator.parse("home/username/my_dataset/participants.tsv")
Traceback (most recent call last):
...
ValueError: Path must be relative to root of a BIDS dataset, ...
>>> validator.parse("/participants.tsv")
{'stem': 'participants', 'extension': '.tsv'}
"""
if cls.regexes is None:
cls._init_regexes()
if path.startswith(os.sep):
path = path.replace(os.sep, '/')
if not path.startswith('/'):
raise ValueError("Path must be relative to root of a BIDS dataset,"
" and must include a leading forward slash `/`.")
for regex in cls.regexes:
match = re.match(regex, path[1:])
if match:
return {k: v for k, v in match.groupdict().items() if v is not None}
return {}
@classmethod
@lru_cache
def is_bids(cls, path):
"""Check if file path adheres to BIDS.
Main method of the validator. Uses other class methods for checking
different aspects of the file path.
Parameters
----------
path : str
Path of a file to be checked. Must be relative to root of a BIDS
dataset, and must include a leading forward slash `/`.
Notes
-----
When you test a file path, make sure that the path is relative to the
root of the BIDS dataset the file is part of. That is, as soon as the
file path contains parts outside of the BIDS dataset, the validation
will fail. For example "home/username/my_dataset/participants.tsv" will
fail, although "/participants.tsv" is a valid BIDS file.
Examples
--------
>>> from bids_validator import BIDSValidator
>>> validator = BIDSValidator()
>>> filepaths = [
... "/sub-01/anat/sub-01_rec-CSD_T1w.nii.gz",
... "/sub-01/anat/sub-01_acq-23_rec-CSD_T1w.exe", # wrong extension
... "home/username/my_dataset/participants.tsv", # not relative to root
... "/participants.tsv",
... ]
>>> for filepath in filepaths:
... print(validator.is_bids(filepath))
True
False
False
True
"""
try:
return cls.parse(path) != {}
except ValueError:
return False
@classmethod
def is_top_level(cls, path):
"""Check if the file has appropriate name for a top-level file."""
parts = cls.parse(path)
if not parts:
return False
return parts.get('subject') is None
def is_associated_data(self, path):
"""Check if file is appropriate associated data."""
if not self.index_associated:
return False
parts = self.parse(path)
if not parts:
return False
return parts.get('path') in ('code', 'derivatives', 'stimuli', 'sourcedata')
@classmethod
def is_session_level(cls, path):
"""Check if the file has appropriate name for a session level."""
parts = cls.parse(path)
if not parts:
return False
return parts.get('datatype') is None and parts.get('suffix') != 'sessions'
@classmethod
def is_subject_level(cls, path):
"""Check if the file has appropriate name for a subject level."""
parts = cls.parse(path)
if not parts:
return False
return parts.get('suffix') == 'sessions'
@classmethod
def is_phenotypic(cls, path):
"""Check if file is phenotypic data."""
parts = cls.parse(path)
if not parts:
return False
return parts.get('datatype') == 'phenotype'
@classmethod
def is_file(cls, path):
"""Check if file is a data file or non-inherited metadata file."""
parts = cls.parse(path)
if not parts:
return False
return parts.get('datatype') not in (None, 'phenotype')