Function _describe_file has a Cognitive Complexity of 41 (exceeds 5 allowed). Consider refactoring.

Open

def _describe_file(dsmeta, fmeta):
    meta = getprop(fmeta, ['metadata'], {})
    bidsmeta = getprop(meta, ['bids'], {})
    suffix = getprop(bidsmeta, ['suffix'], None)
    if suffix is None:

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Function process has a Cognitive Complexity of 29 (exceeds 5 allowed). Consider refactoring.

Open

    def process(self, match):
        """Produce the next token and bit of text.

        Interprets the ANSI code (which may be a color code or some other
        code), changing the lexer state and producing a new token. If it's not

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Function _get_assay_df has a Cognitive Complexity of 28 (exceeds 5 allowed). Consider refactoring.

Open

def _get_assay_df(
        dsmeta,
        modality, protocol_ref, files, file_descr,
        repository_info=None):
    if not repository_info:

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Function get_metadata has a Cognitive Complexity of 27 (exceeds 5 allowed). Consider refactoring.

Open

    def get_metadata(self, dataset, content):
        if not content:
            return {}, []
        contentmeta = []
        log_progress(

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Function cmdline_example_to_rst has a Cognitive Complexity of 27 (exceeds 5 allowed). Consider refactoring.

Open

def cmdline_example_to_rst(src, out=None, ref=None):
    if out is None:
        from six.moves import StringIO
        out = StringIO()

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Function convert has a Cognitive Complexity of 27 (exceeds 5 allowed). Consider refactoring.

Open

def convert(
        dsmeta,
        filemeta,
        output_directory,
        repository_info=None):

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Function _get_cnmeta has a Cognitive Complexity of 23 (exceeds 5 allowed). Consider refactoring.

Open

    def _get_cnmeta(self, bids):
        # TODO any custom handling of participants infos should eventually
        # be done by pybids in one way or another
        path_props = {}
        participants_fname = opj(self.ds.path, 'participants.tsv')

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File bids2scidata.py has 533 lines of code (exceeds 500 allowed). Consider refactoring.

Open

# emacs: -*- mode: python; py-indent-offset: 4; tab-width: 4; indent-tabs-mode: nil -*-
# ex: set sts=4 ts=4 sw=4 noet:
# ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
#
#   See COPYING file distributed along with the datalad package for the

Function yield_participant_info has a Cognitive Complexity of 20 (exceeds 5 allowed). Consider refactoring.

Open

def yield_participant_info(bids):
    for bidsvars in bids.get_collections(
            level='dataset')[0].to_df().to_dict(orient='records'):
        props = dict(id=assure_unicode(bidsvars.pop('subject')))
        for p in bidsvars:

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Function get_metadata has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.

Open

    def get_metadata(self, dataset, content):
        imgseries = {}
        imgs = {}
        log_progress(
            lgr.info,

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Function __call__ has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.

Open

    def __call__(repo_name, repo_accession, repo_url, path=None, output=None, dataset=None):
        # we need this resource file, no point in starting without it
        default_path = opj(dirname(datalad_neuroimaging.__file__), 'resources', 'isatab',
                'scidata_bids_investigator.txt')
        itmpl_path = cfg.obtain(

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Function get_required_content has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.

Open

    def get_required_content(self):
        # TODO: logging
        # bids_dir = _find_bids_root(self.dataset.path)
        for f in REQUIRED_BIDS_FILES:
            f_abs = self.dataset.pathobj / f

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Function _gather_protocol_parameters_from_df has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.

Open

def _gather_protocol_parameters_from_df(df, protocols):
    params = set()
    protos = None
    for i, col in enumerate(list(df.columns) + ['Protocol REF']):
        if col == 'Protocol REF':

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Function color_tokens has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring.

Open

def color_tokens(fg_colors, bg_colors):
    """Return color tokens for a given set of colors.

    Pygments doesn't have a generic "color" token; instead everything is
    contextual (e.g. "comment" or "variable"). That doesn't make sense for us,

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Function _convert_value has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.

Open

def _convert_value(v):
    t = type(v)
    if v is None:
        cv = v
    elif t in (int, float):

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Function __init__ has 8 arguments (exceeds 4 allowed). Consider refactoring.

Open

    def __init__(self,

Avoid deeply nested control flow statements.

Open

                            if fg_color:
                                self.fg_color = fg_color
                            elif bg_color:
                                self.bg_color = bg_color
                            elif value == 1:

Function split_term_source_accession has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

def split_term_source_accession(val):
    if val is None:
        return '', ''
    if not r_url.match(val):
        # no URL

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Function _format_action_invocation has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    def _format_action_invocation(self, action):
        if not action.option_strings:
            metavar, = self._metavar_formatter(action, action.dest)(1)
            return metavar

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Function _get_assay_df has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

def _get_assay_df(