from datetime import datetime import pytest from .conftest import EXAMPLE_DIR_XML_WO_PARAMS, EXAMPLE_DIR_XML_WITH_PARAMS class DummyDataFunc: def __init__(self, as_bool): self.data = None self.as_bool = as_bool def __call__(self, data): self.data = data def __bool__(self): return self.as_bool def test_parser_target_init(): from sensospot_parser.xml_parser import ParserTarget target = ParserTarget() assert target.collected == [] assert target._current == {} assert target._data_func is None @pytest.mark.parametrize( "tag, attributes, expected", [ ("UnknownTag", {"ID": "something"}, {}), ( "ScanJobResult", {"ID": "scan job 1"}, {"Analysis.Name": "scan job 1"}, ), ( "AssayResult", {"ID": "C03"}, {"Well.Name": "C03", "Well.Row": "C", "Well.Column": 3}, ), ("ChannelConfig1", {}, {"Exposure.Id": 1}), ("Spot", {"ID": "456"}, {"Pos.Id": 456}), ( "Result", {"Label": "a label", "Type": "Unknown", "Value": "a value"}, {"a label": "a value"}, ), ], ) @pytest.mark.parametrize("additionals", [{}, {"Ignored": "value"}]) def test_parser_target_start_simple_attributes( tag, attributes, additionals, expected ): from sensospot_parser.xml_parser import ParserTarget target = ParserTarget() attributes.update(additionals) target.start(tag, attributes) # stateful operation assert target._current == expected assert target._data_func is None def test_parser_target_start_timestamp(): from sensospot_parser.xml_parser import ParserTarget target = ParserTarget() target.start("Timestamp", {}) assert target._data_func == target._data_timestamp_parser def test_parser_target_start_image_file_name(): from sensospot_parser.xml_parser import ParserTarget target = ParserTarget() target.start("ImageFileName", {}) assert target._data_func == target._data_image_name_parser @pytest.mark.parametrize( "data_type, value, expected", [ ("unknown type", 1, "1"), ("System.Int32", "12", 12), ("System.UInt32", "23", 23), ("System.Double", "4.56", 4.56), ("System.Boolean", "true", True), ("System.Boolean", "True", True), ("System.Boolean", "Xrue", False), ], ) def test_parser_target_result_attributes_parser(data_type, value, expected): from sensospot_parser.xml_parser import ParserTarget target = ParserTarget() data = {"Label": "some label", "Type": data_type, "Value": value} target._result_attributes_parser(data) # stateful operation assert target._current == {"some label": expected} assert type(target._current["some label"]) == type(expected) @pytest.mark.parametrize( "value, expected", [ ("3/7/2022 5:31:47 PM", datetime(2022, 3, 7, 17, 31, 47)), ("03/7/2022 5:31:47 PM", datetime(2022, 3, 7, 17, 31, 47)), ("3/07/2022 5:31:47 PM", datetime(2022, 3, 7, 17, 31, 47)), ("03/07/2022 5:31:47 PM", datetime(2022, 3, 7, 17, 31, 47)), ("3/7/2022 5:3:47 PM", datetime(2022, 3, 7, 17, 3, 47)), ("3/7/2022 5:31:4 PM", datetime(2022, 3, 7, 17, 31, 4)), ("3/7/2022 5:31:47 pm", datetime(2022, 3, 7, 17, 31, 47)), ("3/7/2022 5:31:47 AM", datetime(2022, 3, 7, 5, 31, 47)), ], ) def test_parser_target_data_timestamp_parser(value, expected): from sensospot_parser.xml_parser import ParserTarget target = ParserTarget() target._data_timestamp_parser(value) # stateful operation assert target._current == {"Analysis.Datetime": expected} def test_parser_target_data_image_name_parser(): from sensospot_parser.xml_parser import ParserTarget target = ParserTarget() target._data_image_name_parser(" some file path ") # stateful operation assert target._current == {"Analysis.Image": "some file path"} def test_parser_target_data_does_not_call_function(): from sensospot_parser.xml_parser import ParserTarget target = ParserTarget() dummy = DummyDataFunc(as_bool=False) target._data_func = dummy target.data("some data") # the NotImplementedError is not raised assert dummy.data is None def test_parser_target_data_does_call_function(): from sensospot_parser.xml_parser import ParserTarget target = ParserTarget() dummy = DummyDataFunc(as_bool=True) target._data_func = dummy target.data("some data") # stateful operation assert dummy.data == "some data" def test_parser_target_data_reacts_on_spot(): from sensospot_parser.xml_parser import ParserTarget target = ParserTarget() target._current = {"some current": "data values"} target.end("Spot") # stateful operation assert target.collected == [{"some current": "data values"}] assert target.collected[0] is not target._current def test_parser_target_data_does_only_react_on_spot(): from sensospot_parser.xml_parser import ParserTarget target = ParserTarget() target._current = {"some current": "data values"} target.end("NonSpotTag") # stateful operation assert target.collected == [] def test_parser_target_closed(): from sensospot_parser.xml_parser import ParserTarget target = ParserTarget() target.closed() # stateful operation, must be callable def test_find_result_xml_file_ok(tmp_path): from sensospot_parser.xml_parser import _find_result_xml_file xls_file = tmp_path / "result.xsl" xls_file.touch() xml_file = tmp_path / "result.xml" xml_file.touch() print(list(tmp_path.iterdir())) result = _find_result_xml_file(tmp_path) assert result == xml_file def test_find_result_xml_file_no_matching_xml_file(tmp_path): from sensospot_parser.xml_parser import _find_result_xml_file xls_file = tmp_path / "result.xsl" xls_file.touch() xml_file = tmp_path / "other.xml" xml_file.touch() result = _find_result_xml_file(tmp_path) assert result is None def test_find_result_xml_file_no_xsl_file(tmp_path): from sensospot_parser.xml_parser import _find_result_xml_file xml_file = tmp_path / "result.xml" xml_file.touch() result = _find_result_xml_file(tmp_path) assert result is None def test_find_result_xml_file_multiple_xsl_files(tmp_path): from sensospot_parser.xml_parser import _find_result_xml_file xls_file = tmp_path / "result.xsl" xls_file.touch() surplus_file = tmp_path / "surplus.xsl" surplus_file.touch() xml_file = tmp_path / "result.xml" xml_file.touch() result = _find_result_xml_file(tmp_path) assert result is None def test_find_result_hidden_xsl_file(tmp_path): from sensospot_parser.xml_parser import _find_result_xml_file xls_file = tmp_path / ".result.xsl" xls_file.touch() xml_file = tmp_path / ".result.xml" xml_file.touch() print(list(tmp_path.iterdir())) result = _find_result_xml_file(tmp_path) assert result is None def test_parse_xml_file_ok(example_dir): import pandas from sensospot_parser.xml_parser import ( parse_xml_file, _find_result_xml_file, ) folder = example_dir / EXAMPLE_DIR_XML_WO_PARAMS xml_file = _find_result_xml_file(folder) result = parse_xml_file(xml_file) assert isinstance(result, pandas.DataFrame) assert len(result) == 4 * 4 * 4 * 100 assert set(result["Well.Row"]) == set("ABCD") assert set(result["Well.Column"]) == {1, 2, 3, 4} assert set(result["Exposure.Id"]) == {1, 2, 3, 4} assert min(result["Spot.Diameter"]) == 22 assert max(result["Spot.Diameter"]) == 34 assert "Parameters.Time" not in result @pytest.mark.parametrize( "file_name, message", [ ("not_existing.xml", "Xml file does not exist"), ("incomplete.xml", "Could not parse assay results xml file"), ("malformed_data.xml", "Malformed data in xml file"), ], ) def test_parse_xml_file_raies_error(file_name, message, example_dir): from sensospot_parser.xml_parser import parse_xml_file xml_file = example_dir / file_name with pytest.raises(ValueError) as e: parse_xml_file(xml_file) assert message in str(e) def test_parse_xml_folder_with_params(example_dir): import pandas from sensospot_parser.xml_parser import parse_xml_folder folder = example_dir / EXAMPLE_DIR_XML_WITH_PARAMS result = parse_xml_folder(folder) assert isinstance(result, pandas.DataFrame) assert len(result) == 4 * 4 * 4 * 100 assert not result["Parameters.Time"].hasnans def test_parse_xml_folder_without_params(example_dir): import pandas from sensospot_parser.xml_parser import parse_xml_folder folder = example_dir / EXAMPLE_DIR_XML_WO_PARAMS result = parse_xml_folder(folder) assert isinstance(result, pandas.DataFrame) assert len(result) == 4 * 4 * 4 * 100 assert result["Parameters.Time"].hasnans def test_parse_xml_folder_non_existing_xml_file(tmp_path): from sensospot_parser.xml_parser import parse_xml_folder with pytest.raises(ValueError) as e: parse_xml_folder(tmp_path) assert "Could not find assay results xml file" in str(e)