"""Test the parsing of headers""" import pytest from hypothesis import given from hypothesis import strategies as st from quality_control.errors import InvalidValue, DuplicateHeading from quality_control.headers import ( invalid_header, invalid_headings, duplicate_headings) @pytest.mark.unit_test @given(headers=st.lists(st.text(max_size=10), max_size=1)) def test_invalid_header_with_list_of_one_value(headers): """Test `invalid_header` with invalid header row""" assert invalid_header("test.file", 0, headers) == InvalidValue( "test.file", 0, 0, "".join(headers), "The header MUST contain at least 2 columns") @pytest.mark.unit_test @given(headings=st.lists(st.text(min_size=2, max_size=10), min_size=2)) def test_invalid_headings_with_invalid_inputs(headings): "Verify that the check for header validity works" assert invalid_headings( "test.file", 0, ("BXD1", "BXD2", "BXD3"), headings) == tuple( InvalidValue("test.file", 0, col, heading, f"'{heading}' not a valid strain.") for col, heading in enumerate(headings, start=2)) @pytest.mark.unit_test @pytest.mark.parametrize( "headers", [ (("ProbeSet", "BXD3", "BXD1")), (("Individual", "AStrain", "AnotherStrain", "YetAnotherStrain"))]) def test_invalid_header_with_valid_headers(headers): "Verify that the check for header validity works" assert invalid_header("test.file", 0, headers) is None @pytest.mark.unit_test @pytest.mark.parametrize( "strains,headings", [ (("BXD1", "BXD2", "BXD3"), ("BXD3", "BXD1")), (("AStrain", "AnotherStrain", "YetAnotherStrain"), ("AStrain", "AnotherStrain", "YetAnotherStrain"))]) def test_invalid_headings_with_valid_headings(strains, headings): "Verify that the check for header validity works" assert invalid_headings("test.file", 0, strains, headings) == tuple() @pytest.mark.unit_test @pytest.mark.parametrize( "headers,repeated", [ (("ProbeSet", "BXD3", "BXD1", "BXD1"), {"BXD1": (3, 4)}), (("Individual", "AStrain", "AnotherStrain", "YetAnotherStrain", "AStrain"), {"AStrain": (2, 5)})]) def test_duplicate_headers_with_repeated_column_headings(headers, repeated): """Check that parsing fails if any header is duplicated""" assert duplicate_headings("test.file", 0, headers) == tuple( DuplicateHeading("test.file", 0, cols, head, ( f"Heading '{head}', is repeated in columns " f"{','.join(str(i) for i in cols)}")) for head, cols in repeated.items()) @pytest.mark.unit_test @pytest.mark.parametrize( "headers", [ (("ProbeSet", "BXD3", "BXD1")), (("Individual", "AStrain", "AnotherStrain", "YetAnotherStrain",))]) def test_duplicate_headers_with_unique_column_headings(headers): """Check that parsing fails if any header is duplicated""" assert duplicate_headings("test.file", 0, headers) == tuple()