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| """BIDS validator common Python package.""" | ||
| from .bids_validator import BIDSValidator | ||
| __all__ = ['BIDSValidator'] | ||
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| from . import _version | ||
| __version__ = _version.get_versions()['version'] |
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| # This file was generated by 'versioneer.py' (0.20) from | ||
| # revision-control system data, or from the parent directory name of an | ||
| # unpacked source archive. Distribution tarballs contain a pre-generated copy | ||
| # of this file. | ||
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| import json | ||
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| version_json = ''' | ||
| { | ||
| "date": "2022-03-28T15:30:05-0500", | ||
| "dirty": false, | ||
| "error": null, | ||
| "full-revisionid": "fd78d856d5b3785456a9eb4659c223f5a15bc512", | ||
| "version": "1.9.3" | ||
| } | ||
| ''' # END VERSION_JSON | ||
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| def get_versions(): | ||
| return json.loads(version_json) |
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| """Validation class for BIDS projects.""" | ||
| import re | ||
| import os | ||
| import json | ||
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| 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. | ||
| """ | ||
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| 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.dir_rules = os.path.join(os.path.dirname(__file__)) + "/rules/" | ||
| self.index_associated = index_associated | ||
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| def is_bids(self, 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. | ||
| 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 | ||
| """ | ||
| conditions = [] | ||
|
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| conditions.append(self.is_top_level(path)) | ||
| conditions.append(self.is_associated_data(path)) | ||
| conditions.append(self.is_session_level(path)) | ||
| conditions.append(self.is_subject_level(path)) | ||
| conditions.append(self.is_phenotypic(path)) | ||
| conditions.append(self.is_file(path)) | ||
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| return (any(conditions)) | ||
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| def is_top_level(self, path): | ||
| """Check if the file has appropriate name for a top-level file.""" | ||
| regexps = self.get_regular_expressions(self.dir_rules + | ||
| 'top_level_rules.json') | ||
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| conditions = [False if re.compile(x).search(path) is None else True for | ||
| x in regexps] | ||
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| return (any(conditions)) | ||
|
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| def is_associated_data(self, path): | ||
| """Check if file is appropriate associated data.""" | ||
| if not self.index_associated: | ||
| return False | ||
|
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| regexps = self.get_regular_expressions(self.dir_rules + | ||
| 'associated_data_rules.json') | ||
|
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| conditions = [(re.compile(x).search(path) is not None) for | ||
| x in regexps] | ||
|
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| return any(conditions) | ||
|
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| def is_session_level(self, path): | ||
| """Check if the file has appropriate name for a session level.""" | ||
| regexps = self.get_regular_expressions(self.dir_rules + | ||
| 'session_level_rules.json') | ||
|
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| conditions = [self.conditional_match(x, path) for x in regexps] | ||
|
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| return (any(conditions)) | ||
|
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| def is_subject_level(self, path): | ||
| """Check if the file has appropriate name for a subject level.""" | ||
| regexps = self.get_regular_expressions(self.dir_rules + | ||
| 'subject_level_rules.json') | ||
|
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| conditions = [(re.compile(x).search(path) is not None) for | ||
| x in regexps] | ||
|
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| return (any(conditions)) | ||
|
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| def is_phenotypic(self, path): | ||
| """Check if file is phenotypic data.""" | ||
| regexps = self.get_regular_expressions(self.dir_rules + | ||
| 'phenotypic_rules.json') | ||
|
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| conditions = [(re.compile(x).search(path) is not None) for | ||
| x in regexps] | ||
|
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| return (any(conditions)) | ||
|
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| def is_file(self, path): | ||
| """Check if file is phenotypic data.""" | ||
| regexps = self.get_regular_expressions(self.dir_rules + | ||
| 'file_level_rules.json') | ||
|
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| conditions = [(re.compile(x).search(path) is not None) for | ||
| x in regexps] | ||
|
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| return (any(conditions)) | ||
|
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| def get_regular_expressions(self, file_name): | ||
| """Read regular expressions from a file.""" | ||
| regexps = [] | ||
|
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| with open(file_name, 'r') as fin: | ||
| rules = json.load(fin) | ||
|
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| for key in list(rules.keys()): | ||
| rule = rules[key] | ||
|
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| regexp = rule["regexp"] | ||
|
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| if "tokens" in rule: | ||
| tokens = rule["tokens"] | ||
|
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| for token in list(tokens): | ||
| regexp = regexp.replace(token, "|".join(tokens[token])) | ||
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| regexps.append(regexp) | ||
|
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| return regexps | ||
|
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| def conditional_match(self, expression, path): | ||
| """Find conditional match.""" | ||
| match = re.compile(expression).findall(path) | ||
| match = match[0] if len(match) >= 1 else False | ||
| # adapted from JS code and JS does not support conditional groups | ||
| if (match): | ||
| if ((match[1] == match[2][1:]) | (not match[1])): | ||
| return True | ||
| else: | ||
| return False | ||
| else: | ||
| return False |
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