Commit fc2ccabf authored by Paul McCarthy's avatar Paul McCarthy 🚵
Browse files

RF: Require at least one entity in a BIDS file name. Do not use realpath on

metadata file name, as files within a BIDS data set may be sym-linked from
another file/directory structure (e.g. datalad/git-annex)
parent 33f85a0a
......@@ -18,6 +18,7 @@
All of the other functions in this module should not be considered part of the
public API.
.. see:: https://bids-specification.readthedocs.io/en/stable/
.. note:: The `pybids <https://bids-standard.github.io/pybids/>`_ library is
a more suitable choice if you are after a more robust and featured
......@@ -36,8 +37,8 @@ import fsl.utils.path as fslpath
class BIDSFile(object):
"""The ``BIDSFile`` class parses and stores the entities and suffix contained
in a BIDS file. See the :func:`parseFilename` function.
"""The ``BIDSFile`` class parses and stores the entities and suffix
contained in a BIDS file. See the :func:`parseFilename` function.
The :meth:`match` method can be used to compare two ``BIDSFile`` instances.
......@@ -91,15 +92,9 @@ class BIDSFile(object):
def parseFilename(filename):
"""Parses a BIDS-like file name. The file name must consist of zero or more
"entities" (alpha-numeric ``name-value`` pairs), a "suffix", all separated
by underscores, and a regular file extension. For example, the following
file::
sub-01_ses-01_task-stim_bold.nii.gz
has suffix ``bold``, entities ``sub=01``, ``ses=01`` and ``task=stim``, and
extension ``.nii.gz``.
"""Parses a BIDS-like file name, returning the entities and suffix encoded
in the name. See the :func:`isBIDSFile` function for an explanation of
what is considered to be a valid BIDS file name.
.. note:: This function assumes that no period (``.``) characters occur in
the body of a BIDS filename.
......@@ -161,13 +156,22 @@ def inBIDSDir(filename):
def isBIDSFile(filename, strict=True):
"""Returns ``True`` if ``filename`` looks like a BIDS image or JSON file.
A BIDS file name must consist of one or more "entities" (alpha-numeric
``name-value`` pairs), a "suffix", all separated by underscores, and a
regular file extension. For example, the following file::
sub-01_ses-01_task-stim_bold.nii.gz
has suffix ``bold``, entities ``sub=01``, ``ses=01`` and ``task=stim``, and
extension ``.nii.gz``.
:arg filename: Name of file to check
:arg strict: If ``True`` (the default), the file must be within a BIDS
dataset directory, as defined by :func:`inBIDSDir`.
"""
name = op.basename(filename)
pattern = r'([a-z0-9]+-[a-z0-9]+_)*([a-z0-9])+\.(.+)'
pattern = r'([a-z0-9]+-[a-z0-9]+_)+([a-z0-9])+\.(.+)'
flags = re.ASCII | re.IGNORECASE
match = re.fullmatch(pattern, name, flags) is not None
......@@ -189,7 +193,7 @@ def loadMetadata(filename):
``filename``
"""
filename = op.realpath(op.abspath(filename))
filename = op.abspath(filename)
bfile = BIDSFile(filename)
dirname = op.dirname(filename)
prevdir = filename
......
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