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Source code for galaxy.tool_util.verify.asserts.tabular

import re
from typing import Optional

from ._util import _assert_number

[docs]def get_first_line(output, comment): """ get the first non-comment and non-empty line """ if comment != "": match = re.search(f"^([^{comment}].*)$", output, flags=re.MULTILINE) else: match = re.search("^(.+)$", output, flags=re.MULTILINE) if match is None: return "" else: return match.group(1)
[docs]def assert_has_n_columns( output, n: Optional[int] = None, delta: int = 0, min: Optional[int] = None, max: Optional[int] = None, sep="\t", comment="", negate: bool = False, ): """Asserts the tabular output contains n columns. The optional sep argument specifies the column seperator used to determine the number of columns. The optional comment argument specifies comment characters""" first_line = get_first_line(output, comment) n_columns = len(first_line.split(sep)) _assert_number( n_columns, n, delta, min, max, negate, "{expected} {n}+-{delta} columns in output", "{expected} the number of columns in output to be in [{min}:{max}]", )