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309 lines
8.6 KiB
309 lines
8.6 KiB
""" Stub file for testing the project """ |
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import numpy |
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import pytest |
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from .conftest import EXAMPLE_DIR_CSV_WITH_PARAMS, EXAMPLE_DIR_CSV_WO_PARAMS |
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@pytest.mark.parametrize( |
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("sub_dir", "file_name"), |
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[ |
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( |
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EXAMPLE_DIR_CSV_WO_PARAMS, |
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"160218_SG2-013-001_Regen1_Cy3-100_1_A1_1.csv", |
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), |
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( |
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EXAMPLE_DIR_CSV_WITH_PARAMS, |
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"160210_SG2-010-001_Regen_cy3100_1_A1_1.csv", |
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), |
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], |
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) |
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def test_parse_csv(example_dir, sub_dir, file_name): |
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from sensospot_parser.csv_parser import _parse_csv |
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result = _parse_csv(example_dir / sub_dir / file_name) |
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columns = { |
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" ID ": numpy.int64, |
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"Pos.X": numpy.int64, |
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"Pos.Y": numpy.int64, |
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"Bkg.Mean": float, |
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"Spot.Mean": float, |
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"Bkg.Median": float, |
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"Spot.Median": float, |
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"Bkg.StdDev": float, |
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"Spot.StdDev": float, |
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"Bkg.Sum": numpy.int64, |
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"Spot.Sum": numpy.int64, |
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"Bkg.Area": numpy.int64, |
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"Spot.Area": numpy.int64, |
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"Spot.Sat. (%)": numpy.int64, |
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"Found": numpy.bool_, |
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"Pos.Nom.X": numpy.int64, |
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"Pos.Nom.Y": numpy.int64, |
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"Dia.": numpy.int64, |
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"Rect.": str, |
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"Contour": object, # ignore the type of contour |
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} |
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assert set(result.columns) == set(columns.keys()) |
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assert len(result[" ID "].unique()) == 100 |
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assert len(result) == 100 |
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for column, value_type in columns.items(): |
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assert isinstance(result[column][0], value_type) |
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def test_parse_csv_no_array(example_dir): |
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from sensospot_parser.csv_parser import _parse_csv |
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result = _parse_csv(example_dir / "no_array_A1_1.csv") |
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assert len(result) == 1 |
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assert result[" ID "][0] == 0 |
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@pytest.mark.parametrize( |
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("provided", "expected"), |
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[("", "."), ("..,", "."), (".,,", ","), ("..,,", ".")], |
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) |
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def test_guess_decimal_separator_returns_correct_separator(provided, expected): |
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from io import StringIO |
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from sensospot_parser.csv_parser import _guess_decimal_separator |
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handle = StringIO(f"header\n{provided}\n") |
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result = _guess_decimal_separator(handle) |
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assert result == expected |
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def test_guess_decimal_separator_rewinds_handle(): |
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from io import StringIO |
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from sensospot_parser.csv_parser import _guess_decimal_separator |
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handle = StringIO("\n".join(["header", "data_line"])) |
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_guess_decimal_separator(handle) |
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assert next(handle) == "header\n" |
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def test_well_regex_ok(): |
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from sensospot_parser.csv_parser import REGEX_WELL |
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result = REGEX_WELL.match("AbC123") |
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assert result["row"] == "AbC" |
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assert result["column"] == "123" |
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@pytest.mark.parametrize("provided", ["", "A", "1", "1A", "-1", "A-"]) |
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def test_well_regex_no_match(provided): |
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from sensospot_parser.csv_parser import REGEX_WELL |
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result = REGEX_WELL.match(provided) |
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assert result is None |
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@pytest.mark.parametrize( |
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("filename", "expected"), |
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[("A1_1.csv", ("A", 1, 1)), ("test/measurement_1_H12_2", ("H", 12, 2))], |
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) |
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def test_extract_measurement_info_ok(filename, expected): |
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from sensospot_parser.csv_parser import _extract_measurement_info |
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result = _extract_measurement_info(filename) |
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assert result == expected |
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@pytest.mark.parametrize("filename", ["wrong_exposure_A1_B", "no_well_XX_1"]) |
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def test_extract_measurement_info_raises_error(filename): |
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from sensospot_parser.csv_parser import _extract_measurement_info |
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with pytest.raises(ValueError): # noqa: PT011 |
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_extract_measurement_info(filename) |
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def test_parse_file(example_file): |
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from sensospot_parser.csv_parser import parse_csv_file |
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result = parse_csv_file(example_file) |
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columns = { |
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"Pos.Id", |
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"Pos.X", |
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"Pos.Y", |
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"Bkg.Mean", |
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"Spot.Mean", |
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"Bkg.Median", |
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"Spot.Median", |
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"Bkg.StdDev", |
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"Spot.StdDev", |
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"Bkg.Sum", |
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"Spot.Sum", |
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"Bkg.Area", |
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"Spot.Area", |
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"Spot.Saturation", |
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"Spot.Found", |
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"Pos.Nom.X", |
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"Pos.Nom.Y", |
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"Spot.Diameter", |
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"Well.Name", |
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"Well.Row", |
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"Well.Column", |
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"Exposure.Id", |
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"Analysis.Name", |
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"Analysis.Image", |
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} |
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assert set(result.columns) == columns |
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assert result["Well.Name"][0] == "A01" |
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assert result["Well.Row"][0] == "A" |
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assert result["Well.Column"][0] == 1 |
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assert result["Exposure.Id"][0] == 1 |
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assert result["Analysis.Name"][0] == "csv_wo_parameters" |
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file_name = "160218_SG2-013-001_Regen1_Cy3-100_1_A1_1.tif" |
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assert result["Analysis.Image"][0] == file_name |
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def test_parse_file_raises_error(example_dir): |
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from sensospot_parser.csv_parser import parse_csv_file |
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csv_file = ( |
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example_dir |
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/ EXAMPLE_DIR_CSV_WITH_PARAMS |
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/ "should_raise_value_error.csv" |
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) |
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with pytest.raises(ValueError): # noqa: PT011 |
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parse_csv_file(csv_file) |
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def test_parse_file_silenced_returns_data_frame(example_file): |
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from sensospot_parser.csv_parser import _parse_csv_file_silenced |
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result = _parse_csv_file_silenced(example_file) |
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assert result["Well.Row"][0] == "A" |
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assert result["Well.Column"][0] == 1 |
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assert result["Exposure.Id"][0] == 1 |
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def test_parse_file_silenced_returns_none_on_error(example_dir): |
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from sensospot_parser.csv_parser import _parse_csv_file_silenced |
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csv_file = ( |
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example_dir |
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/ EXAMPLE_DIR_CSV_WITH_PARAMS |
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/ "should_raise_value_error.csv" |
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) |
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result = _parse_csv_file_silenced(csv_file) |
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assert result is None |
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@pytest.mark.parametrize( |
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"file_list", |
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[ |
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[ |
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"160218_SG2-013-001_Regen1_Cy3-100_1_A1_1.csv", |
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"160218_SG2-013-001_Regen1_Cy3-100_1_A1_2.csv", |
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], |
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["160218_SG2-013-001_Regen1_Cy3-100_1_A1_1.csv"], |
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], |
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) |
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def testparse_multiple_files_ok(example_dir, file_list): |
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from sensospot_parser.csv_parser import parse_multiple_csv_files |
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sub_dir = example_dir / EXAMPLE_DIR_CSV_WO_PARAMS |
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files = [sub_dir / file for file in file_list] |
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data_frame = parse_multiple_csv_files(files) |
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assert len(data_frame) == 100 * len(files) |
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assert len(data_frame["Exposure.Id"].unique()) == len(files) |
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def testparse_multiple_files_empty_file_list(): |
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from sensospot_parser.csv_parser import parse_multiple_csv_files |
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with pytest.raises(ValueError): # noqa: PT011 |
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parse_multiple_csv_files([]) |
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def testparse_multiple_files_empty_array(example_dir): |
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from sensospot_parser.csv_parser import parse_multiple_csv_files |
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files = [example_dir / "no_array_A1_1.csv"] |
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data_frame = parse_multiple_csv_files(files) |
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assert len(data_frame) == 1 |
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def test_find_csv_files(example_dir): |
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from sensospot_parser.csv_parser import find_csv_files |
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result = list(find_csv_files(example_dir / EXAMPLE_DIR_CSV_WITH_PARAMS)) |
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assert len(result) == (36 * 3) + 1 # 36 wells, 3 exposure + one error file |
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assert all(str(item).endswith(".csv") for item in result) |
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assert all(not item.stem.startswith(".") for item in result) |
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def test_parse_folder_no_datetime_records(example_dir): |
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from sensospot_parser.csv_parser import parse_csv_folder |
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data_frame = parse_csv_folder(example_dir / EXAMPLE_DIR_CSV_WITH_PARAMS) |
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assert len(data_frame) == 36 * 3 * 100 |
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assert len(data_frame["Well.Row"].unique()) == 3 |
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assert len(data_frame["Well.Column"].unique()) == 12 |
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assert len(data_frame["Exposure.Id"].unique()) == 3 |
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assert len(data_frame["Pos.Id"].unique()) == 100 |
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assert len(data_frame["Parameters.Channel"].unique()) == 2 |
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assert len(data_frame["Parameters.Time"].unique()) == 3 |
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assert len(data_frame["Analysis.Datetime"].unique()) == 1 |
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def test_sanity_check_ok(example_dir): |
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from sensospot_parser.csv_parser import ( |
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_sanity_check, |
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parse_multiple_csv_files, |
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) |
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sub_dir = example_dir / EXAMPLE_DIR_CSV_WO_PARAMS |
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file_list = [ |
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"160218_SG2-013-001_Regen1_Cy3-100_1_A1_1.csv", |
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"160218_SG2-013-001_Regen1_Cy3-100_1_A1_2.csv", |
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] |
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files = [sub_dir / file for file in file_list] |
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data_frame = parse_multiple_csv_files(files) |
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result = _sanity_check(data_frame) |
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assert len(result) == len(data_frame) |
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def test_sanity_check_raises_value_error(example_dir): |
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from sensospot_parser.csv_parser import ( |
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_sanity_check, |
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parse_multiple_csv_files, |
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) |
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sub_dir = example_dir / EXAMPLE_DIR_CSV_WO_PARAMS |
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file_list = [ |
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"160218_SG2-013-001_Regen1_Cy3-100_1_A1_1.csv", |
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"160218_SG2-013-001_Regen1_Cy3-100_1_A1_2.csv", |
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] |
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files = [sub_dir / file for file in file_list] |
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data_frame = parse_multiple_csv_files(files) |
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data_frame = data_frame.drop(data_frame.index[1]) |
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with pytest.raises(ValueError): # noqa: PT011 |
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_sanity_check(data_frame)
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