diff options
Diffstat (limited to 'tests/qc')
| -rw-r--r-- | tests/qc/test_cells.py | 20 | ||||
| -rw-r--r-- | tests/qc/test_cells_average.py | 2 | ||||
| -rw-r--r-- | tests/qc/test_cells_standard_error.py | 2 | ||||
| -rw-r--r-- | tests/qc/test_error_collection.py | 9 | ||||
| -rw-r--r-- | tests/qc/test_header.py | 25 |
5 files changed, 33 insertions, 25 deletions
diff --git a/tests/qc/test_cells.py b/tests/qc/test_cells.py index e4a0959..937579f 100644 --- a/tests/qc/test_cells.py +++ b/tests/qc/test_cells.py @@ -22,12 +22,12 @@ def test_cell_value_errors_with_invalid_inputs2(num_str): `quality_control.errors.InvalidValue` object which holds the error information. """ - assert avg_invalid_value(0, 0, num_str) == InvalidValue( - 0, 0, num_str, ( + assert avg_invalid_value("test.file", 0, 0, num_str) == InvalidValue( + "test.file", 0, 0, num_str, ( f"Invalid value '{num_str}'. Expected string representing a number " "with exactly three decimal places.")) - assert se_invalid_value(0, 0, num_str) == InvalidValue( - 0, 0, num_str, ( + assert se_invalid_value("test.file", 0, 0, num_str) == InvalidValue( + "test.file", 0, 0, num_str, ( f"Invalid value '{num_str}'. Expected string representing a number " "with at least six decimal places.")) @@ -43,8 +43,8 @@ def test_cell_average_value_errors_if_not_three_decimal_places2(num_str): object with the information about the placement of the invalid value. """ line, col = randint(0, 100), randint(0, 20) - assert avg_invalid_value(line, col, num_str) == InvalidValue( - line, col, num_str, ( + assert avg_invalid_value("test.file", line, col, num_str) == InvalidValue( + "test.file", line, col, num_str, ( f"Invalid value '{num_str}'. Expected string representing a number " "with exactly three decimal places.")) @@ -57,7 +57,7 @@ def test_cell_average_value_pass_if_three_decimal_places(num_str): THEN: `avg_invalid_value` returns `None` """ line, col = randint(0, 100), randint(0, 20) - assert avg_invalid_value(line, col, num_str) is None + assert avg_invalid_value("test.file", line, col, num_str) is None @given(num_str=st.from_regex(r"^[0-9]+\.([0-9]{0,5}$)", fullmatch=True).filter( lambda param: not re.match(r"^[0-9]+\.?0*$", param))) @@ -70,8 +70,8 @@ def test_cell_standard_error_value_errors_if_less_than_six_decimal_places2(num_s object with the information about the placement of the invalid value. """ line, col = randint(0, 100), randint(0, 20) - assert se_invalid_value(line, col, num_str) == InvalidValue( - line, col, num_str, ( + assert se_invalid_value("test.file", line, col, num_str) == InvalidValue( + "test.file", line, col, num_str, ( f"Invalid value '{num_str}'. Expected string representing a number " "with at least six decimal places.")) @@ -84,4 +84,4 @@ def test_cell_standard_error_value_pass_if_six_or_more_decimal_places(num_str): THEN: `se_invalid_value` returns `None` """ line, col = randint(0, 100), randint(0, 20) - assert se_invalid_value(line, col, num_str) is None + assert se_invalid_value("test.file", line, col, num_str) is None diff --git a/tests/qc/test_cells_average.py b/tests/qc/test_cells_average.py index 68fd4ec..b6ded31 100644 --- a/tests/qc/test_cells_average.py +++ b/tests/qc/test_cells_average.py @@ -14,4 +14,4 @@ def test_cell_average_value_pass_if_no_decimal_places(num_str): THEN: `avg_invalid_value` returns `None` """ line, col = randint(0, 100), randint(0, 20) - assert avg_invalid_value(line, col, num_str) is None + assert avg_invalid_value("test.file", line, col, num_str) is None diff --git a/tests/qc/test_cells_standard_error.py b/tests/qc/test_cells_standard_error.py index 90c13cf..fa9f1db 100644 --- a/tests/qc/test_cells_standard_error.py +++ b/tests/qc/test_cells_standard_error.py @@ -17,4 +17,4 @@ def test_cell_standard_error_value_errors_if_less_than_six_decimal_places2(num_s THEN: `se_invalid_value` returns a `None`. """ line, col = randint(0, 100), randint(0, 20) - assert invalid_value(line, col, num_str) is None + assert invalid_value("test.file", line, col, num_str) is None diff --git a/tests/qc/test_error_collection.py b/tests/qc/test_error_collection.py index 962d2c5..260fabf 100644 --- a/tests/qc/test_error_collection.py +++ b/tests/qc/test_error_collection.py @@ -44,11 +44,14 @@ def test_collect_errors(filepath, filetype, strains, count): "filepath,filetype,expected", (("tests/test_data/average_inconsistent_columns.tsv", FileType.AVERAGE, (InconsistentColumns( - 4, 4, 5, "Header row has 4 columns while row 4 has 5 columns"), + "average_inconsistent_columns.tsv", 4, 4, 5, + "Header row has 4 columns while row 4 has 5 columns"), InconsistentColumns( - 5, 4, 3, "Header row has 4 columns while row 5 has 3 columns"), + "average_inconsistent_columns.tsv", 5, 4, 3, + "Header row has 4 columns while row 5 has 3 columns"), InconsistentColumns( - 6, 4, 7, "Header row has 4 columns while row 6 has 7 columns"))),)) + "average_inconsistent_columns.tsv", 6, 4, 7, + "Header row has 4 columns while row 6 has 7 columns"))),)) def test_collect_inconsistent_column_errors(filepath, filetype, strains, expected): """ Given: A file with inconsistent columns in certain lines diff --git a/tests/qc/test_header.py b/tests/qc/test_header.py index 5e54122..06647a2 100644 --- a/tests/qc/test_header.py +++ b/tests/qc/test_header.py @@ -11,17 +11,22 @@ from quality_control.headers import ( @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), + assert invalid_header("test.file", 0, headers) == InvalidValue( + "test.file", 0, 0, "<TAB>".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(0, ("BXD1", "BXD2", "BXD3"), headings) == tuple( - InvalidValue(0, col, heading, f"'{heading}' not a valid strain.") - for col, heading in enumerate(headings, start=2)) + 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( @@ -30,7 +35,7 @@ def test_invalid_headings_with_invalid_inputs(headings): (("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 + assert invalid_header("test.file", 0, headers) is None @pytest.mark.unit_test @pytest.mark.parametrize( @@ -40,7 +45,7 @@ def test_invalid_header_with_valid_headers(headers): ("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() + assert invalid_headings("test.file", 0, strains, headings) == tuple() @pytest.mark.unit_test @pytest.mark.parametrize( @@ -50,8 +55,8 @@ def test_invalid_headings_with_valid_headings(strains, headings): "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, ( + 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()) @@ -63,4 +68,4 @@ def test_duplicate_headers_with_repeated_column_headings(headers, repeated): (("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() + assert duplicate_headings("test.file", 0, headers) == tuple() |