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import csv
from . import NOT_SET, strutil, fsutil
EMPTY = '-'
UNKNOWN = '???'
def parse_markers(markers, default=None):
if markers is NOT_SET:
return default
if not markers:
return None
if type(markers) is not str:
return markers
if markers == markers[0] * len(markers):
return [markers]
return list(markers)
def fix_row(row, **markers):
if isinstance(row, str):
raise NotImplementedError(row)
empty = parse_markers(markers.pop('empty', ('-',)))
unknown = parse_markers(markers.pop('unknown', ('???',)))
row = (val if val else None for val in row)
if not empty:
if unknown:
row = (UNKNOWN if val in unknown else val for val in row)
elif not unknown:
row = (EMPTY if val in empty else val for val in row)
else:
row = (EMPTY if val in empty else (UNKNOWN if val in unknown else val)
for val in row)
return tuple(row)
def _fix_read_default(row):
for value in row:
yield value.strip()
def _fix_write_default(row, empty=''):
for value in row:
yield empty if value is None else str(value)
def _normalize_fix_read(fix):
if fix is None:
fix = ''
if callable(fix):
def fix_row(row):
values = fix(row)
return _fix_read_default(values)
elif isinstance(fix, str):
def fix_row(row):
values = _fix_read_default(row)
return (None if v == fix else v
for v in values)
else:
raise NotImplementedError(fix)
return fix_row
def _normalize_fix_write(fix, empty=''):
if fix is None:
fix = empty
if callable(fix):
def fix_row(row):
values = fix(row)
return _fix_write_default(values, empty)
elif isinstance(fix, str):
def fix_row(row):
return _fix_write_default(row, fix)
else:
raise NotImplementedError(fix)
return fix_row
def read_table(infile, header, *,
sep='\t',
fix=None,
_open=open,
_get_reader=csv.reader,
):
"""Yield each row of the given ???-separated (e.g. tab) file."""
if isinstance(infile, str):
with _open(infile, newline='') as infile:
yield from read_table(
infile,
header,
sep=sep,
fix=fix,
_open=_open,
_get_reader=_get_reader,
)
return
lines = strutil._iter_significant_lines(infile)
# Validate the header.
if not isinstance(header, str):
header = sep.join(header)
try:
actualheader = next(lines).strip()
except StopIteration:
actualheader = ''
if actualheader != header:
raise ValueError(f'bad header {actualheader!r}')
fix_row = _normalize_fix_read(fix)
for row in _get_reader(lines, delimiter=sep or '\t'):
yield tuple(fix_row(row))
def write_table(outfile, header, rows, *,
sep='\t',
fix=None,
backup=True,
_open=open,
_get_writer=csv.writer,
):
"""Write each of the rows to the given ???-separated (e.g. tab) file."""
if backup:
fsutil.create_backup(outfile, backup)
if isinstance(outfile, str):
with _open(outfile, 'w', newline='') as outfile:
return write_table(
outfile,
header,
rows,
sep=sep,
fix=fix,
backup=backup,
_open=_open,
_get_writer=_get_writer,
)
if isinstance(header, str):
header = header.split(sep or '\t')
fix_row = _normalize_fix_write(fix)
writer = _get_writer(outfile, delimiter=sep or '\t')
writer.writerow(header)
for row in rows:
writer.writerow(
tuple(fix_row(row))
)
def parse_table(entries, sep, header=None, rawsep=None, *,
default=NOT_SET,
strict=True,
):
header, sep = _normalize_table_file_props(header, sep)
if not sep:
raise ValueError('missing "sep"')
ncols = None
if header:
if strict:
ncols = len(header.split(sep))
cur_file = None
for line, filename in strutil.parse_entries(entries, ignoresep=sep):
_sep = sep
if filename:
if header and cur_file != filename:
cur_file = filename
# Skip the first line if it's the header.
if line.strip() == header:
continue
else:
# We expected the header.
raise NotImplementedError((header, line))
elif rawsep and sep not in line:
_sep = rawsep
row = _parse_row(line, _sep, ncols, default)
if strict and not ncols:
ncols = len(row)
yield row, filename
def parse_row(line, sep, *, ncols=None, default=NOT_SET):
if not sep:
raise ValueError('missing "sep"')
return _parse_row(line, sep, ncols, default)
def _parse_row(line, sep, ncols, default):
row = tuple(v.strip() for v in line.split(sep))
if (ncols or 0) > 0:
diff = ncols - len(row)
if diff:
if default is NOT_SET or diff < 0:
raise Exception(f'bad row (expected {ncols} columns, got {row!r})')
row += (default,) * diff
return row
def _normalize_table_file_props(header, sep):
if not header:
return None, sep
if not isinstance(header, str):
if not sep:
raise NotImplementedError(header)
header = sep.join(header)
elif not sep:
for sep in ('\t', ',', ' '):
if sep in header:
break
else:
sep = None
return header, sep
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