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"""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)
@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(0, headers) == InvalidValue(
0, 0, "<TAB>".join(headers),
"The header MUST contain at least 2 columns")
@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(0, ("BXD1", "BXD2", "BXD3"), headings) == tuple(
InvalidValue(0, col, heading, f"'{heading}' not a valid strain.")
for col, heading in enumerate(headings, start=2))
@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(0, headers) is None
@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(0, strains, headings) == tuple()
@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(0, headers) == tuple(
DuplicateHeading(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.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(0, headers) == tuple()
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