From 873091504c7abe05eb147819c03bade34ca67b36 Mon Sep 17 00:00:00 2001 From: Holger Frey Date: Tue, 3 Jan 2023 11:47:17 +0100 Subject: [PATCH 01/11] renamed the "parser" module to "csv_parser" The "csv_parser" module will be used as a backup if the analysis xml file is not present. --- src/sensospot_parser/__init__.py | 2 +- .../{parser.py => csv_parser.py} | 0 tests/{test_parser.py => test_csv_parser.py} | 42 +++++++++---------- 3 files changed, 22 insertions(+), 22 deletions(-) rename src/sensospot_parser/{parser.py => csv_parser.py} (100%) rename tests/{test_parser.py => test_csv_parser.py} (86%) diff --git a/src/sensospot_parser/__init__.py b/src/sensospot_parser/__init__.py index 8124da2..8450620 100644 --- a/src/sensospot_parser/__init__.py +++ b/src/sensospot_parser/__init__.py @@ -12,7 +12,7 @@ import click import pandas from . import columns # noqa: F401 -from .parser import parse_file, parse_folder # noqa: F401 +from .csv_parser import parse_file, parse_folder # noqa: F401 DEFAULT_OUTPUT_FILENAME = "collected_data.csv" diff --git a/src/sensospot_parser/parser.py b/src/sensospot_parser/csv_parser.py similarity index 100% rename from src/sensospot_parser/parser.py rename to src/sensospot_parser/csv_parser.py diff --git a/tests/test_parser.py b/tests/test_csv_parser.py similarity index 86% rename from tests/test_parser.py rename to tests/test_csv_parser.py index c9659b1..4ab9480 100644 --- a/tests/test_parser.py +++ b/tests/test_csv_parser.py @@ -25,7 +25,7 @@ from .conftest import ( ], ) def test_parse_csv(example_dir, sub_dir, file_name): - from sensospot_parser.parser import _parse_csv + from sensospot_parser.csv_parser import _parse_csv result = _parse_csv(example_dir / sub_dir / file_name) @@ -60,7 +60,7 @@ def test_parse_csv(example_dir, sub_dir, file_name): def test_parse_csv_no_array(example_dir): - from sensospot_parser.parser import _parse_csv + from sensospot_parser.csv_parser import _parse_csv result = _parse_csv(example_dir / "no_array_A1_1.csv") @@ -74,7 +74,7 @@ def test_parse_csv_no_array(example_dir): def test_guess_decimal_separator_returns_correct_separator(input, expected): from io import StringIO - from sensospot_parser.parser import _guess_decimal_separator + from sensospot_parser.csv_parser import _guess_decimal_separator handle = StringIO(f"header\n{input}\n") result = _guess_decimal_separator(handle) @@ -85,7 +85,7 @@ def test_guess_decimal_separator_returns_correct_separator(input, expected): def test_guess_decimal_separator_rewinds_handle(): from io import StringIO - from sensospot_parser.parser import _guess_decimal_separator + from sensospot_parser.csv_parser import _guess_decimal_separator handle = StringIO("\n".join(["header", "data_line"])) _guess_decimal_separator(handle) @@ -94,7 +94,7 @@ def test_guess_decimal_separator_rewinds_handle(): def test_well_regex_ok(): - from sensospot_parser.parser import REGEX_WELL + from sensospot_parser.csv_parser import REGEX_WELL result = REGEX_WELL.match("AbC123") @@ -104,7 +104,7 @@ def test_well_regex_ok(): @pytest.mark.parametrize("input", ["", "A", "1", "1A", "-1", "A-"]) def test_well_regex_no_match(input): - from sensospot_parser.parser import REGEX_WELL + from sensospot_parser.csv_parser import REGEX_WELL result = REGEX_WELL.match(input) @@ -116,7 +116,7 @@ def test_well_regex_no_match(input): [("A1_1.csv", ("A", 1, 1)), ("test/measurement_1_H12_2", ("H", 12, 2))], ) def test_extract_measurement_info_ok(filename, expected): - from sensospot_parser.parser import _extract_measurement_info + from sensospot_parser.csv_parser import _extract_measurement_info result = _extract_measurement_info(filename) @@ -125,7 +125,7 @@ def test_extract_measurement_info_ok(filename, expected): @pytest.mark.parametrize("filename", ["wrong_exposure_A1_B", "no_well_XX_1"]) def test_extract_measurement_info_raises_error(filename): - from sensospot_parser.parser import _extract_measurement_info + from sensospot_parser.csv_parser import _extract_measurement_info with pytest.raises(ValueError): _extract_measurement_info(filename) @@ -134,7 +134,7 @@ def test_extract_measurement_info_raises_error(filename): def test_cleanup_data_columns(): from pandas import DataFrame - from sensospot_parser.parser import _cleanup_data_columns + from sensospot_parser.csv_parser import _cleanup_data_columns columns = ["Rect.", "Contour", " ID ", "Found", "Dia."] data = {col: [i] for i, col in enumerate(columns)} @@ -149,7 +149,7 @@ def test_cleanup_data_columns(): def test_parse_file(example_file): - from sensospot_parser.parser import parse_file + from sensospot_parser.csv_parser import parse_file result = parse_file(example_file) @@ -191,7 +191,7 @@ def test_parse_file(example_file): def test_parse_file_raises_error(example_dir): - from sensospot_parser.parser import parse_file + from sensospot_parser.csv_parser import parse_file csv_file = ( example_dir / EXAMPLE_DIR_WITH_PARAMS / "should_raise_value_error.csv" @@ -202,7 +202,7 @@ def test_parse_file_raises_error(example_dir): def test_parse_file_silenced_returns_data_frame(example_file): - from sensospot_parser.parser import _parse_file_silenced + from sensospot_parser.csv_parser import _parse_file_silenced result = _parse_file_silenced(example_file) @@ -212,7 +212,7 @@ def test_parse_file_silenced_returns_data_frame(example_file): def test_parse_file_silenced_returns_none_on_error(example_dir): - from sensospot_parser.parser import _parse_file_silenced + from sensospot_parser.csv_parser import _parse_file_silenced csv_file = ( example_dir / EXAMPLE_DIR_WITH_PARAMS / "should_raise_value_error.csv" @@ -234,7 +234,7 @@ def test_parse_file_silenced_returns_none_on_error(example_dir): ], ) def testparse_multiple_files_ok(example_dir, file_list): - from sensospot_parser.parser import parse_multiple_files + from sensospot_parser.csv_parser import parse_multiple_files sub_dir = example_dir / EXAMPLE_DIR_WO_PARAMS files = [sub_dir / file for file in file_list] @@ -247,14 +247,14 @@ def testparse_multiple_files_ok(example_dir, file_list): def testparse_multiple_files_empty_file_list(): - from sensospot_parser.parser import parse_multiple_files + from sensospot_parser.csv_parser import parse_multiple_files with pytest.raises(ValueError): parse_multiple_files([]) def testparse_multiple_files_empty_array(example_dir): - from sensospot_parser.parser import parse_multiple_files + from sensospot_parser.csv_parser import parse_multiple_files files = [example_dir / "no_array_A1_1.csv"] @@ -265,7 +265,7 @@ def testparse_multiple_files_empty_array(example_dir): def test_find_csv_files(example_dir): - from sensospot_parser.parser import find_csv_files + from sensospot_parser.csv_parser import find_csv_files result = list(find_csv_files(example_dir / EXAMPLE_DIR_WITH_PARAMS)) @@ -275,7 +275,7 @@ def test_find_csv_files(example_dir): def test_parse_folder_no_datetime_records(example_dir): - from sensospot_parser.parser import parse_folder + from sensospot_parser.csv_parser import parse_folder data_frame = parse_folder(example_dir / EXAMPLE_DIR_WITH_PARAMS) @@ -290,7 +290,7 @@ def test_parse_folder_no_datetime_records(example_dir): def test_parse_folder_with_datetime_records(example_dir): - from sensospot_parser.parser import parse_folder + from sensospot_parser.csv_parser import parse_folder data_frame = parse_folder(example_dir / EXAMPLE_DIR_WITH_RECORD) @@ -305,7 +305,7 @@ def test_parse_folder_with_datetime_records(example_dir): def test_sanity_check_ok(example_dir): - from sensospot_parser.parser import _sanity_check, parse_multiple_files + from sensospot_parser.csv_parser import _sanity_check, parse_multiple_files sub_dir = example_dir / EXAMPLE_DIR_WO_PARAMS file_list = [ @@ -321,7 +321,7 @@ def test_sanity_check_ok(example_dir): def test_sanity_check_raises_value_error(example_dir): - from sensospot_parser.parser import _sanity_check, parse_multiple_files + from sensospot_parser.csv_parser import _sanity_check, parse_multiple_files sub_dir = example_dir / EXAMPLE_DIR_WO_PARAMS file_list = [ From 938b0630690150d07a0e5e8d7af15e747d2f7d37 Mon Sep 17 00:00:00 2001 From: Holger Frey Date: Tue, 3 Jan 2023 11:55:31 +0100 Subject: [PATCH 02/11] removed the "recordtime" module The "recordtime" module uses the assay result xml file for retrieving the Analyses.Datetime value. This value is only available in the assay result xml. Since the "parse_csv" module will only be a backup if this xml file is not present, a separate parser for the Analysis.Datetime is not needed anymore --- src/sensospot_parser/csv_parser.py | 8 ++- src/sensospot_parser/recordtime.py | 98 ------------------------------ tests/test_csv_parser.py | 21 +------ tests/test_recordtime.py | 98 ------------------------------ 4 files changed, 7 insertions(+), 218 deletions(-) delete mode 100644 src/sensospot_parser/recordtime.py delete mode 100644 tests/test_recordtime.py diff --git a/src/sensospot_parser/csv_parser.py b/src/sensospot_parser/csv_parser.py index 73f0656..d59518c 100644 --- a/src/sensospot_parser/csv_parser.py +++ b/src/sensospot_parser/csv_parser.py @@ -12,7 +12,6 @@ import pandas from . import columns from .parameters import add_measurement_parameters -from .recordtime import add_record_time PathLike = Union[str, pathlib.Path] @@ -225,8 +224,13 @@ def parse_folder(folder: PathLike, quiet: bool = False) -> pandas.DataFrame: data_frame = parse_multiple_files(file_list) except ValueError: raise ValueError(f"No sensospot data found in folder '{folder}'") + data_frame = add_measurement_parameters(data_frame, folder_path) - data_frame = add_record_time(data_frame, folder_path) + + # The csv parser is only used if the xml analysis file is not present + # the xml file would hold the Analysis.Datetime value + data_frame[columns.ANALYSIS_DATETIME] = None + if quiet: return data_frame return _sanity_check(data_frame) diff --git a/src/sensospot_parser/recordtime.py b/src/sensospot_parser/recordtime.py deleted file mode 100644 index 6bda6c8..0000000 --- a/src/sensospot_parser/recordtime.py +++ /dev/null @@ -1,98 +0,0 @@ -""" Sensospot Data Parser - -Parsing the numerical output from Sensovations Sensospot image analysis. -""" - -import pathlib -from typing import Tuple, Union, Iterable, Optional - -import numpy -import pandas -from defusedxml import ElementTree - -from . import columns - -PathLike = Union[str, pathlib.Path] - - -def _search_records_file(folder: PathLike) -> Optional[pathlib.Path]: - """searches for a the records xml file in a folder - - Args: - folder: directory to search - - Returns: - the path to the settings file or None - """ - folder_path = pathlib.Path(folder) - files = (item for item in folder_path.iterdir() if item.suffix == ".xsl") - xls_files = [path for path in files if not path.name.startswith(".")] - if len(xls_files) == 1: - xml_file = xls_files[0].with_suffix(".xml") - if xml_file.is_file(): - return xml_file - return None - - -def _iter_records(records_file: PathLike) -> Iterable[Tuple[str, str]]: - """parses the information from a records file - - Args: - records_file: path to the records file - - Yields: - tuples, filename as first element and the datetime string as second - """ - records_path = pathlib.Path(records_file) - tree = ElementTree.parse(records_path) - for channel_config in tree.findall(".//*[ImageFileName]"): - image_tag = channel_config.find("ImageFileName") - image_name = None if image_tag is None else image_tag.text - datetime_tag = channel_config.find("Timestamp") - datetime_str = None if datetime_tag is None else datetime_tag.text - yield image_name, datetime_str - - -def _parse_records_file(records_file: PathLike) -> pandas.DataFrame: - """parses the information from a records file - - Args: - records_file: path to the records file - - Returns: - pandas data frame with the parsed information - """ - data = _iter_records(records_file) - data_frame = pandas.DataFrame( - data, columns=[columns.ANALYSIS_IMAGE, columns.ANALYSIS_DATETIME] - ) - data_frame[columns.ANALYSIS_DATETIME] = pandas.to_datetime( - data_frame[columns.ANALYSIS_DATETIME] - ) - return data_frame - - -def add_record_time( - measurement: pandas.DataFrame, folder: PathLike -) -> pandas.DataFrame: - """adds the recoding datetime to the data frame - - The returned DataFrame will contain one more column for parsed datetime - - If the parameters could not be foundor do not match up with the - measurement data, the additional collumn will contain NaN. - - Argumentss: - measurement: the parsed measurement data - folder: the folder of the measurement data - - Returns: - the measurement data with parameters added - """ - record_path = _search_records_file(folder) - if record_path is None: - measurement[columns.ANALYSIS_DATETIME] = numpy.NAN - return measurement - - data_frame = _parse_records_file(record_path) - return measurement.merge(data_frame, how="left", on=columns.ANALYSIS_IMAGE) diff --git a/tests/test_csv_parser.py b/tests/test_csv_parser.py index 4ab9480..04b0190 100644 --- a/tests/test_csv_parser.py +++ b/tests/test_csv_parser.py @@ -4,11 +4,7 @@ import numpy import pytest -from .conftest import ( - EXAMPLE_DIR_WO_PARAMS, - EXAMPLE_DIR_WITH_PARAMS, - EXAMPLE_DIR_WITH_RECORD, -) +from .conftest import EXAMPLE_DIR_WO_PARAMS, EXAMPLE_DIR_WITH_PARAMS @pytest.mark.parametrize( @@ -289,21 +285,6 @@ def test_parse_folder_no_datetime_records(example_dir): assert len(data_frame["Analysis.Datetime"].unique()) == 1 -def test_parse_folder_with_datetime_records(example_dir): - from sensospot_parser.csv_parser import parse_folder - - data_frame = parse_folder(example_dir / EXAMPLE_DIR_WITH_RECORD) - - assert len(data_frame) == 8 * 4 * 100 - assert len(data_frame["Well.Row"].unique()) == 2 - assert len(data_frame["Well.Column"].unique()) == 4 - assert len(data_frame["Exposure.Id"].unique()) == 4 - assert len(data_frame["Pos.Id"].unique()) == 100 - assert len(data_frame["Parameters.Channel"].unique()) == 1 - assert len(data_frame["Parameters.Time"].unique()) == 1 - assert len(data_frame["Analysis.Datetime"].unique()) == 8 - - def test_sanity_check_ok(example_dir): from sensospot_parser.csv_parser import _sanity_check, parse_multiple_files diff --git a/tests/test_recordtime.py b/tests/test_recordtime.py deleted file mode 100644 index 6a998da..0000000 --- a/tests/test_recordtime.py +++ /dev/null @@ -1,98 +0,0 @@ -import pandas -import pytest - -from .conftest import EXAMPLE_DIR_WITH_PARAMS, EXAMPLE_DIR_WITH_RECORD - - -@pytest.fixture -def file_list(example_dir): - import pathlib - - path = pathlib.Path(example_dir / EXAMPLE_DIR_WITH_RECORD) - tifs = (i.with_suffix(".tif") for i in path.glob("*.csv")) - return [i.name for i in tifs] - - -def test_search_records_file_ok(example_dir): - from sensospot_parser.recordtime import _search_records_file - - result = _search_records_file(example_dir / EXAMPLE_DIR_WITH_RECORD) - - assert result.suffix == ".xml" - - -def test_search_records_file_not_found(example_dir): - from sensospot_parser.recordtime import _search_records_file - - result = _search_records_file(example_dir / EXAMPLE_DIR_WITH_PARAMS) - - assert result is None - - -def test_iter_records(example_dir): - from sensospot_parser.recordtime import _iter_records, _search_records_file - - path = _search_records_file(example_dir / EXAMPLE_DIR_WITH_RECORD) - - result = list(_iter_records(path)) - - assert ( - result[0][0] == "220307_SN0801_CHECK-01_SL1,11,9,14_MS_1_1_A01_1.tif" - ) - assert result[0][1] == "3/7/2022 5:31:47 PM" - assert ( - result[-1][0] == "220307_SN0801_CHECK-01_SL1,11,9,14_MS_1_1_D04_4.tif" - ) - assert result[-1][1] == "3/7/2022 5:33:41 PM" - - -def test_parse_records_file(example_dir): - from sensospot_parser.recordtime import ( - _parse_records_file, - _search_records_file, - ) - - path = _search_records_file(example_dir / EXAMPLE_DIR_WITH_RECORD) - - result = _parse_records_file(path) - - assert isinstance(result, pandas.DataFrame) - assert list(result.columns) == ["Analysis.Image", "Analysis.Datetime"] - assert len(result) == 64 - - -def test_add_record_time_ok(example_dir, file_list): - from sensospot_parser.recordtime import add_record_time - - df = pandas.DataFrame(file_list, columns=["Analysis.Image"]) - - result = add_record_time(df, example_dir / EXAMPLE_DIR_WITH_RECORD) - - assert len(df) == len(result) - assert list(result.columns) == ["Analysis.Image", "Analysis.Datetime"] - assert not result["Analysis.Datetime"].hasnans - - -def test_add_record_time_unknown_file(example_dir, file_list): - from sensospot_parser.recordtime import add_record_time - - extended_list = file_list + ["unknown file"] - df = pandas.DataFrame(extended_list, columns=["Analysis.Image"]) - - result = add_record_time(df, example_dir / EXAMPLE_DIR_WITH_RECORD) - - assert len(df) == len(result) - assert list(result.columns) == ["Analysis.Image", "Analysis.Datetime"] - assert result["Analysis.Datetime"].hasnans - - -def test_add_record_time_no_record_xml(example_dir, file_list): - from sensospot_parser.recordtime import add_record_time - - df = pandas.DataFrame(file_list, columns=["Analysis.Image"]) - - result = add_record_time(df, example_dir / EXAMPLE_DIR_WITH_PARAMS) - - assert len(df) == len(result) - assert list(result.columns) == ["Analysis.Image", "Analysis.Datetime"] - assert result["Analysis.Datetime"].hasnans From 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xml_with_parameters}/220307_SN0801_CHECK-01_SL1,11,9,14_MS_1_1.xsl (100%) rename example_data/{record_time => xml_with_parameters}/220307_SN0801_CHECK-01_SL1,11,9,14_MS_1_1_A01.xml (100%) create mode 100644 example_data/xml_with_parameters/Parameters/Assay/S QC 10x10 Cy3 100ms Cy5 150-15ms/S QC 10x10 Cy3 100ms Cy5 150-15ms.svalg create mode 100644 example_data/xml_with_parameters/Parameters/Assay/S QC 10x10 Cy3 100ms Cy5 150-15ms/S QC 10x10 Cy3 100ms Cy5 150-15ms.svary create mode 100644 example_data/xml_with_parameters/Parameters/Assay/S QC 10x10 Cy3 100ms Cy5 150-15ms/S QC 10x10 Cy3 100ms Cy5 150-15ms.svexp create mode 100644 example_data/xml_with_parameters/Parameters/PlateHolder/SinglePlateHolder.svph create mode 100644 example_data/xml_with_parameters/Parameters/Rack/Microplate (96 wells).svmpd create mode 100644 example_data/xml_wo_parameters/220307_SN0801_CHECK-01_SL1,11,9,14_MS_1_1.xml create mode 100644 example_data/xml_wo_parameters/220307_SN0801_CHECK-01_SL1,11,9,14_MS_1_1.xsl create mode 100644 example_data/xml_wo_parameters/220307_SN0801_CHECK-01_SL1,11,9,14_MS_1_1_A01.xml diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 55ad1bb..372083c 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -33,7 +33,7 @@ repos: pass_filenames: false - id: flake8 name: flake8 test - entry: flake8 --ignore S101 tests + entry: flake8 --ignore S101,W503 tests language: system pass_filenames: false - id: pytest diff --git a/Makefile b/Makefile index 866a958..be53078 100644 --- a/Makefile +++ b/Makefile @@ -58,7 +58,7 @@ lint: ## reformat with black and check style with flake8 isort tests black src tests flake8 --ignore E231,W503,E402 src - flake8 --ignore S101 tests + flake8 --ignore S101,W503 tests test: lint ## run tests quickly, stop on first error pytest tests -x -l --last-failed --disable-warnings -m "not functional" diff --git 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a/example_data/mtp_wo_parameters/160218_SG2-013-001_Regen1_Cy3-100_1_H9_3.csv b/example_data/csv_wo_parameters/160218_SG2-013-001_Regen1_Cy3-100_1_H9_3.csv old mode 100755 new mode 100644 similarity index 100% rename from example_data/mtp_wo_parameters/160218_SG2-013-001_Regen1_Cy3-100_1_H9_3.csv rename to example_data/csv_wo_parameters/160218_SG2-013-001_Regen1_Cy3-100_1_H9_3.csv diff --git a/example_data/record_time/220307_SN0801_CHECK-01_SL1,11,9,14_MS_1_1_A01_1.csv b/example_data/record_time/220307_SN0801_CHECK-01_SL1,11,9,14_MS_1_1_A01_1.csv deleted file mode 100644 index 40b4226..0000000 --- a/example_data/record_time/220307_SN0801_CHECK-01_SL1,11,9,14_MS_1_1_A01_1.csv +++ /dev/null @@ -1,101 +0,0 @@ - ID Pos.X Pos.Y Bkg.Mean Spot.Mean Bkg.Median Spot.Median Bkg.StdDev Spot.StdDev Bkg.Sum Spot.Sum Bkg.Area Spot.Area Spot.Sat. 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+ + + + + + + + 220307_SN0801_CHECK-01_SL1,11,9,14_MS_1_1_A01_4.tif + + + + \ No newline at end of file diff --git a/tests/conftest.py b/tests/conftest.py index 19d2ce6..8e4d43c 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -5,9 +5,10 @@ from pathlib import Path import pandas import pytest -EXAMPLE_DIR_WO_PARAMS = "mtp_wo_parameters" -EXAMPLE_DIR_WITH_PARAMS = "mtp_with_parameters" -EXAMPLE_DIR_WITH_RECORD = "record_time" +EXAMPLE_DIR_CSV_WO_PARAMS = "csv_wo_parameters" +EXAMPLE_DIR_CSV_WITH_PARAMS = "csv_with_parameters" +EXAMPLE_DIR_XML_WO_RECORD = "xml_wo_parameters" +EXAMPLE_DIR_XML_WITH_RECORD = "xml_wo_parameters" @pytest.fixture(scope="session") @@ -18,7 +19,7 @@ def example_dir(request): @pytest.fixture def example_file(example_dir): - data_dir = example_dir / EXAMPLE_DIR_WO_PARAMS + data_dir = example_dir / EXAMPLE_DIR_CSV_WO_PARAMS yield data_dir / "160218_SG2-013-001_Regen1_Cy3-100_1_A1_1.csv" @@ -93,16 +94,16 @@ def normalization_data_frame(): @pytest.fixture(scope="session") def parsed_data_frame_with_params(example_dir): - from sensospot_parser.parser import parse_folder + from sensospot_parser.csv_parser import parse_folder - return parse_folder(example_dir / EXAMPLE_DIR_WITH_PARAMS) + return parse_folder(example_dir / EXAMPLE_DIR_CSV_WITH_PARAMS) @pytest.fixture(scope="session") def parsed_data_frame_without_params(example_dir): - from sensospot_parser.parser import parse_folder + from sensospot_parser.csv_parser import parse_folder - return parse_folder(example_dir / EXAMPLE_DIR_WO_PARAMS) + return parse_folder(example_dir / EXAMPLE_DIR_CSV_WO_PARAMS) @pytest.fixture diff --git a/tests/test_csv_parser.py b/tests/test_csv_parser.py index 04b0190..e5f3cf6 100644 --- a/tests/test_csv_parser.py +++ b/tests/test_csv_parser.py @@ -4,18 +4,18 @@ import numpy import pytest -from .conftest import EXAMPLE_DIR_WO_PARAMS, EXAMPLE_DIR_WITH_PARAMS +from .conftest import EXAMPLE_DIR_CSV_WO_PARAMS, EXAMPLE_DIR_CSV_WITH_PARAMS @pytest.mark.parametrize( "sub_dir, file_name", [ ( - EXAMPLE_DIR_WO_PARAMS, + EXAMPLE_DIR_CSV_WO_PARAMS, "160218_SG2-013-001_Regen1_Cy3-100_1_A1_1.csv", ), ( - EXAMPLE_DIR_WITH_PARAMS, + EXAMPLE_DIR_CSV_WITH_PARAMS, "160210_SG2-010-001_Regen_cy3100_1_A1_1.csv", ), ], @@ -181,7 +181,7 @@ def test_parse_file(example_file): assert result["Well.Row"][0] == "A" assert result["Well.Column"][0] == 1 assert result["Exposure.Id"][0] == 1 - assert result["Analysis.Name"][0] == "mtp_wo_parameters" + assert result["Analysis.Name"][0] == "csv_wo_parameters" file_name = "160218_SG2-013-001_Regen1_Cy3-100_1_A1_1.tif" assert result["Analysis.Image"][0] == file_name @@ -190,7 +190,9 @@ def test_parse_file_raises_error(example_dir): from sensospot_parser.csv_parser import parse_file csv_file = ( - example_dir / EXAMPLE_DIR_WITH_PARAMS / "should_raise_value_error.csv" + example_dir + / EXAMPLE_DIR_CSV_WITH_PARAMS + / "should_raise_value_error.csv" ) with pytest.raises(ValueError): @@ -211,7 +213,9 @@ def test_parse_file_silenced_returns_none_on_error(example_dir): from sensospot_parser.csv_parser import _parse_file_silenced csv_file = ( - example_dir / EXAMPLE_DIR_WITH_PARAMS / "should_raise_value_error.csv" + example_dir + / EXAMPLE_DIR_CSV_WITH_PARAMS + / "should_raise_value_error.csv" ) result = _parse_file_silenced(csv_file) @@ -232,7 +236,7 @@ def test_parse_file_silenced_returns_none_on_error(example_dir): def testparse_multiple_files_ok(example_dir, file_list): from sensospot_parser.csv_parser import parse_multiple_files - sub_dir = example_dir / EXAMPLE_DIR_WO_PARAMS + sub_dir = example_dir / EXAMPLE_DIR_CSV_WO_PARAMS files = [sub_dir / file for file in file_list] data_frame = parse_multiple_files(files) @@ -263,7 +267,7 @@ def testparse_multiple_files_empty_array(example_dir): def test_find_csv_files(example_dir): from sensospot_parser.csv_parser import find_csv_files - result = list(find_csv_files(example_dir / EXAMPLE_DIR_WITH_PARAMS)) + result = list(find_csv_files(example_dir / EXAMPLE_DIR_CSV_WITH_PARAMS)) assert len(result) == (36 * 3) + 1 # 36 wells, 3 exposure + one error file assert all(str(item).endswith(".csv") for item in result) @@ -273,7 +277,7 @@ def test_find_csv_files(example_dir): def test_parse_folder_no_datetime_records(example_dir): from sensospot_parser.csv_parser import parse_folder - data_frame = parse_folder(example_dir / EXAMPLE_DIR_WITH_PARAMS) + data_frame = parse_folder(example_dir / EXAMPLE_DIR_CSV_WITH_PARAMS) assert len(data_frame) == 36 * 3 * 100 assert len(data_frame["Well.Row"].unique()) == 3 @@ -288,7 +292,7 @@ def test_parse_folder_no_datetime_records(example_dir): def test_sanity_check_ok(example_dir): from sensospot_parser.csv_parser import _sanity_check, parse_multiple_files - sub_dir = example_dir / EXAMPLE_DIR_WO_PARAMS + sub_dir = example_dir / EXAMPLE_DIR_CSV_WO_PARAMS file_list = [ "160218_SG2-013-001_Regen1_Cy3-100_1_A1_1.csv", "160218_SG2-013-001_Regen1_Cy3-100_1_A1_2.csv", @@ -304,7 +308,7 @@ def test_sanity_check_ok(example_dir): def test_sanity_check_raises_value_error(example_dir): from sensospot_parser.csv_parser import _sanity_check, parse_multiple_files - sub_dir = example_dir / EXAMPLE_DIR_WO_PARAMS + sub_dir = example_dir / EXAMPLE_DIR_CSV_WO_PARAMS file_list = [ "160218_SG2-013-001_Regen1_Cy3-100_1_A1_1.csv", "160218_SG2-013-001_Regen1_Cy3-100_1_A1_2.csv", diff --git a/tests/test_parameters.py b/tests/test_parameters.py index b91fd92..ea291e4 100644 --- a/tests/test_parameters.py +++ b/tests/test_parameters.py @@ -1,12 +1,12 @@ import pandas -from .conftest import EXAMPLE_DIR_WO_PARAMS, EXAMPLE_DIR_WITH_PARAMS +from .conftest import EXAMPLE_DIR_CSV_WO_PARAMS, EXAMPLE_DIR_CSV_WITH_PARAMS def test_search_params_file_ok(example_dir): from sensospot_parser.parameters import _search_params_file - result = _search_params_file(example_dir / EXAMPLE_DIR_WITH_PARAMS) + result = _search_params_file(example_dir / EXAMPLE_DIR_CSV_WITH_PARAMS) assert result.suffix == ".svexp" @@ -14,7 +14,7 @@ def test_search_params_file_ok(example_dir): def test_search_params_file_no_parameters_folder(example_dir): from sensospot_parser.parameters import _search_params_file - result = _search_params_file(example_dir / EXAMPLE_DIR_WO_PARAMS) + result = _search_params_file(example_dir / EXAMPLE_DIR_CSV_WO_PARAMS) assert result is None @@ -36,7 +36,7 @@ def test_parse_channel_info(example_dir): _parse_measurement_params, ) - params = _search_params_file(example_dir / EXAMPLE_DIR_WITH_PARAMS) + params = _search_params_file(example_dir / EXAMPLE_DIR_CSV_WITH_PARAMS) result = _parse_measurement_params(params) expected = pandas.DataFrame( @@ -53,7 +53,7 @@ def test_parse_channel_info(example_dir): def test_get_measurement_params_file_found(example_dir): from sensospot_parser.parameters import get_measurement_params - result = get_measurement_params(example_dir / EXAMPLE_DIR_WITH_PARAMS) + result = get_measurement_params(example_dir / EXAMPLE_DIR_CSV_WITH_PARAMS) expected = pandas.DataFrame( { @@ -69,7 +69,7 @@ def test_get_measurement_params_file_found(example_dir): def test_get_measurement_params_file_not_found(example_dir): from sensospot_parser.parameters import get_measurement_params - result = get_measurement_params(example_dir / EXAMPLE_DIR_WO_PARAMS) + result = get_measurement_params(example_dir / EXAMPLE_DIR_CSV_WO_PARAMS) assert result is None @@ -77,7 +77,7 @@ def test_get_measurement_params_file_not_found(example_dir): def test_add_measurement_parameters_with_params_file(exposure_df, example_dir): from sensospot_parser.parameters import add_measurement_parameters - folder = example_dir / EXAMPLE_DIR_WITH_PARAMS + folder = example_dir / EXAMPLE_DIR_CSV_WITH_PARAMS exposure_df = add_measurement_parameters(exposure_df, folder) expected = [(1, "green", 100), (2, "red", 150), (3, "red", 15)] @@ -93,7 +93,7 @@ def test_add_measurement_parameters_without_params_file( ): from sensospot_parser.parameters import add_measurement_parameters - folder = example_dir / EXAMPLE_DIR_WO_PARAMS + folder = example_dir / EXAMPLE_DIR_CSV_WO_PARAMS exposure_df = add_measurement_parameters(exposure_df, folder) for exposure_id in range(1, 4): From 8644a25d780cd2f312d2e1c9e2f48abb1a21f0ca Mon Sep 17 00:00:00 2001 From: Holger Frey Date: Tue, 3 Jan 2023 16:27:27 +0100 Subject: [PATCH 04/11] moved _cleanup_data_columns() function to "columns" module by moving this function it can be easily reused in the upcoming "xml_parser" module --- src/sensospot_parser/columns.py | 18 ++++++++++++++++++ src/sensospot_parser/csv_parser.py | 18 ++---------------- tests/test_columns.py | 15 +++++++++++++++ tests/test_csv_parser.py | 17 ----------------- 4 files changed, 35 insertions(+), 33 deletions(-) create mode 100644 tests/test_columns.py diff --git a/src/sensospot_parser/columns.py b/src/sensospot_parser/columns.py index 9897d32..ad63ed8 100644 --- a/src/sensospot_parser/columns.py +++ b/src/sensospot_parser/columns.py @@ -1,5 +1,7 @@ """ Column name definitions """ +import pandas + # original, unmodified column names POS_X = "Pos.X" POS_Y = "Pos.Y" @@ -121,3 +123,19 @@ INDEX_COLUMNS_POS = ( WELL_ROW, POS_ID, ) + + +def _cleanup_data_columns(data_frame: pandas.DataFrame) -> pandas.DataFrame: + """renames some data columns for consistency and drops unused columns + + Args: + data_frame: pandas DataFrame with parsed measurement data + + Returns: + pandas DataFrame, column names cleaned up + """ + renamed = data_frame.rename(columns=CSV_RENAME_MAP) + surplus_columns = set(renamed.columns) - PARSED_DATA_COLUMN_SET + x = renamed.drop(columns=surplus_columns) + print(PARSED_DATA_COLUMN_SET - set(x.columns)) + return x diff --git a/src/sensospot_parser/csv_parser.py b/src/sensospot_parser/csv_parser.py index d59518c..24b29c2 100644 --- a/src/sensospot_parser/csv_parser.py +++ b/src/sensospot_parser/csv_parser.py @@ -1,6 +1,6 @@ """ Sensospot Data Parser -Parsing the numerical output from Sensovations Sensospot image analysis. +Parsing the csv result files from Sensovations Sensospot image analysis. """ import re @@ -84,20 +84,6 @@ def _extract_measurement_info(data_file: PathLike) -> FileInfo: return FileInfo(row, column, exposure) -def _cleanup_data_columns(data_frame: pandas.DataFrame) -> pandas.DataFrame: - """renames some data columns for consistency and drops unused columns - - Args: - data_frame: pandas DataFrame with parsed measurement data - - Returns: - pandas DataFrame, column names cleaned up - """ - renamed = data_frame.rename(columns=columns.CSV_RENAME_MAP) - surplus_columns = set(renamed.columns) - columns.PARSED_DATA_COLUMN_SET - return renamed.drop(columns=surplus_columns) - - def parse_file(data_file: PathLike) -> pandas.DataFrame: """parses one data file and adds metadata to result @@ -124,7 +110,7 @@ def parse_file(data_file: PathLike) -> pandas.DataFrame: data_frame[columns.EXPOSURE_ID] = measurement_info.exposure data_frame[columns.ANALYSIS_NAME] = data_path.parent.name data_frame[columns.ANALYSIS_IMAGE] = data_path.with_suffix(".tif").name - return _cleanup_data_columns(data_frame) + return columns._cleanup_data_columns(data_frame) def _parse_file_silenced(data_file: PathLike) -> Optional[pandas.DataFrame]: diff --git a/tests/test_columns.py b/tests/test_columns.py new file mode 100644 index 0000000..499c221 --- /dev/null +++ b/tests/test_columns.py @@ -0,0 +1,15 @@ +def test_cleanup_data_columns(): + from pandas import DataFrame + + from sensospot_parser.columns import _cleanup_data_columns + + columns = ["Rect.", "Contour", " ID ", "Found", "Dia."] + data = {col: [i] for i, col in enumerate(columns)} + data_frame = DataFrame(data=data) + + result = _cleanup_data_columns(data_frame) + + assert set(result.columns) == {"Pos.Id", "Spot.Found", "Spot.Diameter"} + assert result["Pos.Id"][0] == 2 + assert result["Spot.Found"][0] == 3 + assert result["Spot.Diameter"][0] == 4 diff --git a/tests/test_csv_parser.py b/tests/test_csv_parser.py index e5f3cf6..c8678d3 100644 --- a/tests/test_csv_parser.py +++ b/tests/test_csv_parser.py @@ -127,23 +127,6 @@ def test_extract_measurement_info_raises_error(filename): _extract_measurement_info(filename) -def test_cleanup_data_columns(): - from pandas import DataFrame - - from sensospot_parser.csv_parser import _cleanup_data_columns - - columns = ["Rect.", "Contour", " ID ", "Found", "Dia."] - data = {col: [i] for i, col in enumerate(columns)} - data_frame = DataFrame(data=data) - - result = _cleanup_data_columns(data_frame) - - assert set(result.columns) == {"Pos.Id", "Spot.Found", "Spot.Diameter"} - assert result["Pos.Id"][0] == 2 - assert result["Spot.Found"][0] == 3 - assert result["Spot.Diameter"][0] == 4 - - def test_parse_file(example_file): from sensospot_parser.csv_parser import parse_file From 988c7562d9ad28594a9ecf5e0164f9466fba5aeb Mon Sep 17 00:00:00 2001 From: Holger Frey Date: Tue, 3 Jan 2023 17:00:58 +0100 Subject: [PATCH 05/11] renamed some functions in "csv_parser" module to have more explicit names --- .../S QC 10x10 Cy3 100ms Cy5 150-15ms.svalg | 25 ---------- .../S QC 10x10 Cy3 100ms Cy5 150-15ms.svary | 27 ----------- .../S QC 10x10 Cy3 100ms Cy5 150-15ms.svexp | 19 -------- src/sensospot_parser/__init__.py | 4 +- src/sensospot_parser/csv_parser.py | 20 +++++--- tests/conftest.py | 8 ++-- tests/test_csv_parser.py | 46 +++++++++++-------- tests/test_sensospot_data.py | 4 +- 8 files changed, 47 insertions(+), 106 deletions(-) delete mode 100644 example_data/xml_with_parameters/Parameters/Assay/S QC 10x10 Cy3 100ms Cy5 150-15ms/S QC 10x10 Cy3 100ms Cy5 150-15ms.svalg delete mode 100644 example_data/xml_with_parameters/Parameters/Assay/S QC 10x10 Cy3 100ms Cy5 150-15ms/S QC 10x10 Cy3 100ms Cy5 150-15ms.svary delete mode 100644 example_data/xml_with_parameters/Parameters/Assay/S QC 10x10 Cy3 100ms Cy5 150-15ms/S QC 10x10 Cy3 100ms Cy5 150-15ms.svexp diff --git a/example_data/xml_with_parameters/Parameters/Assay/S QC 10x10 Cy3 100ms Cy5 150-15ms/S QC 10x10 Cy3 100ms Cy5 150-15ms.svalg b/example_data/xml_with_parameters/Parameters/Assay/S QC 10x10 Cy3 100ms Cy5 150-15ms/S QC 10x10 Cy3 100ms Cy5 150-15ms.svalg deleted file mode 100644 index ffa263a..0000000 --- a/example_data/xml_with_parameters/Parameters/Assay/S QC 10x10 Cy3 100ms Cy5 150-15ms/S QC 10x10 Cy3 100ms Cy5 150-15ms.svalg +++ /dev/null @@ -1,25 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/example_data/xml_with_parameters/Parameters/Assay/S QC 10x10 Cy3 100ms Cy5 150-15ms/S QC 10x10 Cy3 100ms Cy5 150-15ms.svary b/example_data/xml_with_parameters/Parameters/Assay/S QC 10x10 Cy3 100ms Cy5 150-15ms/S QC 10x10 Cy3 100ms Cy5 150-15ms.svary deleted file mode 100644 index fc336c3..0000000 --- a/example_data/xml_with_parameters/Parameters/Assay/S QC 10x10 Cy3 100ms Cy5 150-15ms/S QC 10x10 Cy3 100ms Cy5 150-15ms.svary +++ /dev/null @@ -1,27 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/example_data/xml_with_parameters/Parameters/Assay/S QC 10x10 Cy3 100ms Cy5 150-15ms/S QC 10x10 Cy3 100ms Cy5 150-15ms.svexp b/example_data/xml_with_parameters/Parameters/Assay/S QC 10x10 Cy3 100ms Cy5 150-15ms/S QC 10x10 Cy3 100ms Cy5 150-15ms.svexp deleted file mode 100644 index 33be21d..0000000 --- a/example_data/xml_with_parameters/Parameters/Assay/S QC 10x10 Cy3 100ms Cy5 150-15ms/S QC 10x10 Cy3 100ms Cy5 150-15ms.svexp +++ /dev/null @@ -1,19 +0,0 @@ - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/src/sensospot_parser/__init__.py b/src/sensospot_parser/__init__.py index 8450620..74c69ab 100644 --- a/src/sensospot_parser/__init__.py +++ b/src/sensospot_parser/__init__.py @@ -12,7 +12,7 @@ import click import pandas from . import columns # noqa: F401 -from .csv_parser import parse_file, parse_folder # noqa: F401 +from .csv_parser import parse_csv_file, parse_csv_folder # noqa: F401 DEFAULT_OUTPUT_FILENAME = "collected_data.csv" @@ -51,7 +51,7 @@ def main(sources, output, quiet=False): """ paths = (pathlib.Path(source) for source in sources) - collection = (parse_folder(source, quiet) for source in paths) + collection = (parse_csv_folder(source, quiet) for source in paths) result = pandas.concat(collection, ignore_index=True).to_csv( output, sep="\t", index=False ) diff --git a/src/sensospot_parser/csv_parser.py b/src/sensospot_parser/csv_parser.py index 24b29c2..13ef0ce 100644 --- a/src/sensospot_parser/csv_parser.py +++ b/src/sensospot_parser/csv_parser.py @@ -84,7 +84,7 @@ def _extract_measurement_info(data_file: PathLike) -> FileInfo: return FileInfo(row, column, exposure) -def parse_file(data_file: PathLike) -> pandas.DataFrame: +def parse_csv_file(data_file: PathLike) -> pandas.DataFrame: """parses one data file and adds metadata to result will race a ValueError, if metadata could not be extracted @@ -113,7 +113,9 @@ def parse_file(data_file: PathLike) -> pandas.DataFrame: return columns._cleanup_data_columns(data_frame) -def _parse_file_silenced(data_file: PathLike) -> Optional[pandas.DataFrame]: +def _parse_csv_file_silenced( + data_file: PathLike, +) -> Optional[pandas.DataFrame]: """parses one data file and adds metadata Safety checks are supressed @@ -125,12 +127,14 @@ def _parse_file_silenced(data_file: PathLike) -> Optional[pandas.DataFrame]: pandas data frame with the parsed data or None on error """ try: - return parse_file(data_file) + return parse_csv_file(data_file) except ValueError: return None -def parse_multiple_files(file_list: Sequence[PathLike]) -> pandas.DataFrame: +def parse_multiple_csv_files( + file_list: Sequence[PathLike], +) -> pandas.DataFrame: """parses a list of file paths to one combined data frame Args: @@ -140,7 +144,7 @@ def parse_multiple_files(file_list: Sequence[PathLike]) -> pandas.DataFrame: """ if not file_list: raise ValueError("Empty file list provided") - collection = (_parse_file_silenced(path) for path in file_list) + collection = (_parse_csv_file_silenced(path) for path in file_list) filtered = (frame for frame in collection if frame is not None) data_frame = pandas.concat(filtered, ignore_index=True).reset_index() data_frame[columns.WELL_ROW] = data_frame[columns.WELL_ROW].astype( @@ -191,7 +195,9 @@ def _sanity_check(data_frame: pandas.DataFrame) -> pandas.DataFrame: return data_frame -def parse_folder(folder: PathLike, quiet: bool = False) -> pandas.DataFrame: +def parse_csv_folder( + folder: PathLike, quiet: bool = False +) -> pandas.DataFrame: """parses all csv files in a folder to one large dataframe Will raise an ValueError, if no sensospot data could be found in @@ -207,7 +213,7 @@ def parse_folder(folder: PathLike, quiet: bool = False) -> pandas.DataFrame: folder_path = pathlib.Path(folder) file_list = find_csv_files(folder_path) try: - data_frame = parse_multiple_files(file_list) + data_frame = parse_multiple_csv_files(file_list) except ValueError: raise ValueError(f"No sensospot data found in folder '{folder}'") diff --git a/tests/conftest.py b/tests/conftest.py index 8e4d43c..d176031 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -94,16 +94,16 @@ def normalization_data_frame(): @pytest.fixture(scope="session") def parsed_data_frame_with_params(example_dir): - from sensospot_parser.csv_parser import parse_folder + from sensospot_parser.csv_parser import parse_csv_folder - return parse_folder(example_dir / EXAMPLE_DIR_CSV_WITH_PARAMS) + return parse_csv_folder(example_dir / EXAMPLE_DIR_CSV_WITH_PARAMS) @pytest.fixture(scope="session") def parsed_data_frame_without_params(example_dir): - from sensospot_parser.csv_parser import parse_folder + from sensospot_parser.csv_parser import parse_csv_folder - return parse_folder(example_dir / EXAMPLE_DIR_CSV_WO_PARAMS) + return parse_csv_folder(example_dir / EXAMPLE_DIR_CSV_WO_PARAMS) @pytest.fixture diff --git a/tests/test_csv_parser.py b/tests/test_csv_parser.py index c8678d3..371bf7f 100644 --- a/tests/test_csv_parser.py +++ b/tests/test_csv_parser.py @@ -128,9 +128,9 @@ def test_extract_measurement_info_raises_error(filename): def test_parse_file(example_file): - from sensospot_parser.csv_parser import parse_file + from sensospot_parser.csv_parser import parse_csv_file - result = parse_file(example_file) + result = parse_csv_file(example_file) columns = { "Pos.Id", @@ -170,7 +170,7 @@ def test_parse_file(example_file): def test_parse_file_raises_error(example_dir): - from sensospot_parser.csv_parser import parse_file + from sensospot_parser.csv_parser import parse_csv_file csv_file = ( example_dir @@ -179,13 +179,13 @@ def test_parse_file_raises_error(example_dir): ) with pytest.raises(ValueError): - parse_file(csv_file) + parse_csv_file(csv_file) def test_parse_file_silenced_returns_data_frame(example_file): - from sensospot_parser.csv_parser import _parse_file_silenced + from sensospot_parser.csv_parser import _parse_csv_file_silenced - result = _parse_file_silenced(example_file) + result = _parse_csv_file_silenced(example_file) assert result["Well.Row"][0] == "A" assert result["Well.Column"][0] == 1 @@ -193,7 +193,7 @@ def test_parse_file_silenced_returns_data_frame(example_file): def test_parse_file_silenced_returns_none_on_error(example_dir): - from sensospot_parser.csv_parser import _parse_file_silenced + from sensospot_parser.csv_parser import _parse_csv_file_silenced csv_file = ( example_dir @@ -201,7 +201,7 @@ def test_parse_file_silenced_returns_none_on_error(example_dir): / "should_raise_value_error.csv" ) - result = _parse_file_silenced(csv_file) + result = _parse_csv_file_silenced(csv_file) assert result is None @@ -217,12 +217,12 @@ def test_parse_file_silenced_returns_none_on_error(example_dir): ], ) def testparse_multiple_files_ok(example_dir, file_list): - from sensospot_parser.csv_parser import parse_multiple_files + from sensospot_parser.csv_parser import parse_multiple_csv_files sub_dir = example_dir / EXAMPLE_DIR_CSV_WO_PARAMS files = [sub_dir / file for file in file_list] - data_frame = parse_multiple_files(files) + data_frame = parse_multiple_csv_files(files) print(data_frame["Exposure.Id"].unique()) assert len(data_frame) == 100 * len(files) @@ -230,18 +230,18 @@ def testparse_multiple_files_ok(example_dir, file_list): def testparse_multiple_files_empty_file_list(): - from sensospot_parser.csv_parser import parse_multiple_files + from sensospot_parser.csv_parser import parse_multiple_csv_files with pytest.raises(ValueError): - parse_multiple_files([]) + parse_multiple_csv_files([]) def testparse_multiple_files_empty_array(example_dir): - from sensospot_parser.csv_parser import parse_multiple_files + from sensospot_parser.csv_parser import parse_multiple_csv_files files = [example_dir / "no_array_A1_1.csv"] - data_frame = parse_multiple_files(files) + data_frame = parse_multiple_csv_files(files) print(data_frame["Exposure.Id"].unique()) assert len(data_frame) == 1 @@ -258,9 +258,9 @@ def test_find_csv_files(example_dir): def test_parse_folder_no_datetime_records(example_dir): - from sensospot_parser.csv_parser import parse_folder + from sensospot_parser.csv_parser import parse_csv_folder - data_frame = parse_folder(example_dir / EXAMPLE_DIR_CSV_WITH_PARAMS) + data_frame = parse_csv_folder(example_dir / EXAMPLE_DIR_CSV_WITH_PARAMS) assert len(data_frame) == 36 * 3 * 100 assert len(data_frame["Well.Row"].unique()) == 3 @@ -273,7 +273,10 @@ def test_parse_folder_no_datetime_records(example_dir): def test_sanity_check_ok(example_dir): - from sensospot_parser.csv_parser import _sanity_check, parse_multiple_files + from sensospot_parser.csv_parser import ( + _sanity_check, + parse_multiple_csv_files, + ) sub_dir = example_dir / EXAMPLE_DIR_CSV_WO_PARAMS file_list = [ @@ -281,7 +284,7 @@ def test_sanity_check_ok(example_dir): "160218_SG2-013-001_Regen1_Cy3-100_1_A1_2.csv", ] files = [sub_dir / file for file in file_list] - data_frame = parse_multiple_files(files) + data_frame = parse_multiple_csv_files(files) result = _sanity_check(data_frame) @@ -289,7 +292,10 @@ def test_sanity_check_ok(example_dir): def test_sanity_check_raises_value_error(example_dir): - from sensospot_parser.csv_parser import _sanity_check, parse_multiple_files + from sensospot_parser.csv_parser import ( + _sanity_check, + parse_multiple_csv_files, + ) sub_dir = example_dir / EXAMPLE_DIR_CSV_WO_PARAMS file_list = [ @@ -297,7 +303,7 @@ def test_sanity_check_raises_value_error(example_dir): "160218_SG2-013-001_Regen1_Cy3-100_1_A1_2.csv", ] files = [sub_dir / file for file in file_list] - data_frame = parse_multiple_files(files) + data_frame = parse_multiple_csv_files(files) data_frame = data_frame.drop(data_frame.index[1]) with pytest.raises(ValueError): diff --git a/tests/test_sensospot_data.py b/tests/test_sensospot_data.py index 549de0d..a8a2e16 100644 --- a/tests/test_sensospot_data.py +++ b/tests/test_sensospot_data.py @@ -4,5 +4,5 @@ def test_import_api(): from sensospot_parser import main # noqa: F401 from sensospot_parser import columns # noqa: F401 - from sensospot_parser import parse_file # noqa: F401 - from sensospot_parser import parse_folder # noqa: F401 + from sensospot_parser import parse_csv_file # noqa: F401 + from sensospot_parser import parse_csv_folder # noqa: F401 From 8c591e9f3c394fe226b7142ce479f4664baafbcf Mon Sep 17 00:00:00 2001 From: Holger Frey Date: Tue, 3 Jan 2023 17:41:47 +0100 Subject: [PATCH 06/11] removed debug print statement --- src/sensospot_parser/columns.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/src/sensospot_parser/columns.py b/src/sensospot_parser/columns.py index ad63ed8..5d4391e 100644 --- a/src/sensospot_parser/columns.py +++ b/src/sensospot_parser/columns.py @@ -136,6 +136,4 @@ def _cleanup_data_columns(data_frame: pandas.DataFrame) -> pandas.DataFrame: """ renamed = data_frame.rename(columns=CSV_RENAME_MAP) surplus_columns = set(renamed.columns) - PARSED_DATA_COLUMN_SET - x = renamed.drop(columns=surplus_columns) - print(PARSED_DATA_COLUMN_SET - set(x.columns)) - return x + return renamed.drop(columns=surplus_columns) From dd476bb19adebca2875788f63cb97764e9305991 Mon Sep 17 00:00:00 2001 From: Holger Frey Date: Tue, 3 Jan 2023 17:42:40 +0100 Subject: [PATCH 07/11] added more calls to "clenup_data_columns()" to remove double index columns after merges --- src/sensospot_parser/csv_parser.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/sensospot_parser/csv_parser.py b/src/sensospot_parser/csv_parser.py index 13ef0ce..267bfea 100644 --- a/src/sensospot_parser/csv_parser.py +++ b/src/sensospot_parser/csv_parser.py @@ -223,6 +223,8 @@ def parse_csv_folder( # the xml file would hold the Analysis.Datetime value data_frame[columns.ANALYSIS_DATETIME] = None + data_frame = columns._cleanup_data_columns(data_frame) + if quiet: return data_frame return _sanity_check(data_frame) From 819358977e6eb31182f2ecfaa21e15937ddef3a1 Mon Sep 17 00:00:00 2001 From: Holger Frey Date: Tue, 3 Jan 2023 17:43:31 +0100 Subject: [PATCH 08/11] fixed test data for upcoming module xml_parser --- example_data/defect.xml | 29 ++++ .../Calibration Check 4e.svalg | 29 ++++ .../Calibration Check 4e.svary | 131 ++++++++++++++++++ .../Calibration Check 4e.svexp | 21 +++ .../Parameters/Rack/Calibration Slide.svmpd | 21 +++ .../Rack/Microplate (96 wells).svmpd | 21 --- 6 files changed, 231 insertions(+), 21 deletions(-) create mode 100644 example_data/defect.xml create mode 100644 example_data/xml_with_parameters/Parameters/Assay/Calibration Check 4e/Calibration Check 4e.svalg create mode 100644 example_data/xml_with_parameters/Parameters/Assay/Calibration Check 4e/Calibration Check 4e.svary create mode 100644 example_data/xml_with_parameters/Parameters/Assay/Calibration Check 4e/Calibration Check 4e.svexp create mode 100644 example_data/xml_with_parameters/Parameters/Rack/Calibration Slide.svmpd delete mode 100644 example_data/xml_with_parameters/Parameters/Rack/Microplate (96 wells).svmpd diff --git a/example_data/defect.xml b/example_data/defect.xml new file mode 100644 index 0000000..eac8561 --- /dev/null +++ b/example_data/defect.xml @@ -0,0 +1,29 @@ + + + + 3/7/2022 5:31:40 PM + 3/7/2022 5:33:45 PM + + + + + + + Cy3/Cy5 Green + 3/7/2022 5:31:47 PM + 220307_SN0801_CHECK-01_SL1,11,9,14_MS_1_1_A01_1.tif + 150.3716670323235 + 150.6109 + + 150.66990076589988 + -0.62607054037768517 + 0.62607054037768517 + 150.66990076589988 + 227.22602466270919 + 233.1385439330713 + + + + + + \ No newline at end of file diff --git a/example_data/xml_with_parameters/Parameters/Assay/Calibration Check 4e/Calibration Check 4e.svalg b/example_data/xml_with_parameters/Parameters/Assay/Calibration Check 4e/Calibration Check 4e.svalg new file mode 100644 index 0000000..1530523 --- /dev/null +++ b/example_data/xml_with_parameters/Parameters/Assay/Calibration Check 4e/Calibration Check 4e.svalg @@ -0,0 +1,29 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/example_data/xml_with_parameters/Parameters/Assay/Calibration Check 4e/Calibration Check 4e.svary b/example_data/xml_with_parameters/Parameters/Assay/Calibration Check 4e/Calibration Check 4e.svary new file mode 100644 index 0000000..da00932 --- /dev/null +++ b/example_data/xml_with_parameters/Parameters/Assay/Calibration Check 4e/Calibration Check 4e.svary @@ -0,0 +1,131 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/example_data/xml_with_parameters/Parameters/Assay/Calibration Check 4e/Calibration Check 4e.svexp b/example_data/xml_with_parameters/Parameters/Assay/Calibration Check 4e/Calibration Check 4e.svexp new file mode 100644 index 0000000..b62b882 --- /dev/null +++ b/example_data/xml_with_parameters/Parameters/Assay/Calibration Check 4e/Calibration Check 4e.svexp @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/example_data/xml_with_parameters/Parameters/Rack/Calibration Slide.svmpd b/example_data/xml_with_parameters/Parameters/Rack/Calibration Slide.svmpd new file mode 100644 index 0000000..a39226b --- /dev/null +++ b/example_data/xml_with_parameters/Parameters/Rack/Calibration Slide.svmpd @@ -0,0 +1,21 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/example_data/xml_with_parameters/Parameters/Rack/Microplate (96 wells).svmpd b/example_data/xml_with_parameters/Parameters/Rack/Microplate (96 wells).svmpd deleted file mode 100644 index 5695a27..0000000 --- a/example_data/xml_with_parameters/Parameters/Rack/Microplate (96 wells).svmpd +++ /dev/null @@ -1,21 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file From 9de0a0955706989357fa54788809f3390d9b9d51 Mon Sep 17 00:00:00 2001 From: Holger Frey Date: Wed, 4 Jan 2023 12:15:48 +0100 Subject: [PATCH 09/11] added more example xml data for testing --- example_data/malformed_data.xml | 8 ++++++++ 1 file changed, 8 insertions(+) create mode 100644 example_data/malformed_data.xml diff --git a/example_data/malformed_data.xml b/example_data/malformed_data.xml new file mode 100644 index 0000000..8d0639a --- /dev/null +++ b/example_data/malformed_data.xml @@ -0,0 +1,8 @@ + + + + + + + + \ No newline at end of file From 0a1da70021bc9a6889bc3b070d26df45e0b7b735 Mon Sep 17 00:00:00 2001 From: Holger Frey Date: Wed, 4 Jan 2023 13:23:02 +0100 Subject: [PATCH 10/11] added more example data for comparing xml to csv parsing --- ...0801_CHECK-01_SL1,11,9,14_MS_1_1_A01_1.csv | 101 ++++++++++++++++++ ...0801_CHECK-01_SL1,11,9,14_MS_1_1_A01_2.csv | 101 ++++++++++++++++++ ...0801_CHECK-01_SL1,11,9,14_MS_1_1_A01_3.csv | 101 ++++++++++++++++++ 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8169daeb891374a265412c32527de6b5fb56e7a5 Mon Sep 17 00:00:00 2001 From: Holger Frey Date: Wed, 4 Jan 2023 13:35:25 +0100 Subject: [PATCH 11/11] Added parser for the assay results xml file The `sensospot_parser.parse_folder()` function now tries to parse the xml file first and will fall back to parsing csv files if an error occurs --- README.md | 14 +- src/sensospot_parser/__init__.py | 40 +++- src/sensospot_parser/xml_parser.py | 192 ++++++++++++++++ tests/conftest.py | 4 +- tests/test_sensospot_data.py | 44 +++- tests/test_xml_parser.py | 341 +++++++++++++++++++++++++++++ 6 files changed, 621 insertions(+), 14 deletions(-) create mode 100644 src/sensospot_parser/xml_parser.py create mode 100644 tests/test_xml_parser.py diff --git a/README.md b/README.md index f2a7ee0..cd7a5fc 100644 --- a/README.md +++ b/README.md @@ -44,12 +44,16 @@ There is a `columns` module available, providing constans that define the column ## Avaliable public functions: - **parse_folder(path_to_folder)** + Tries the `parse_xml_folder()` function first and if an error occurs, + it falls back to the `parse_csv_folder()` + - **parse_xml_folder(path_to_folder)** + Searches the folder for a parsable Sensospot XML result file and parses it into + a pandas data frame. It will add additional meta data from parameters folder, + if it is present. + - **parse_csv_folder(path_to_folder)** Searches the folder for parsable Sensospot .csv files, parses them into one big pandas data frame and will add additional meta data from parameters folder, if it is present. -- **parse_file(path_to_csv_file)** - Parses a Sensospot csv file into a pandas data frame and will add some additional - meta data from the file name. Is internally also used by `parse_folder()` ## CLI @@ -63,8 +67,8 @@ Arguments: SOURCES: One or more folders with Sensospot measurements Options: - -o, --output FILE Output file path, defaults to 'collected_data.csv' - -q, --quiet Ignore Sanity Check + -o, --output FILE Output file path, defaults to 'collected_data.csv' + -q, --quiet Ignore sanity check for csv file parsing --help Show this message and exit. ``` diff --git a/src/sensospot_parser/__init__.py b/src/sensospot_parser/__init__.py index 74c69ab..9a8cf36 100644 --- a/src/sensospot_parser/__init__.py +++ b/src/sensospot_parser/__init__.py @@ -3,19 +3,43 @@ Parsing the numerical output from Sensovations Sensospot image analysis. """ -__version__ = "1.0.1" +__version__ = "2.0.0" import pathlib +from typing import Union import click import pandas from . import columns # noqa: F401 -from .csv_parser import parse_csv_file, parse_csv_folder # noqa: F401 +from .csv_parser import parse_csv_folder +from .xml_parser import parse_xml_folder DEFAULT_OUTPUT_FILENAME = "collected_data.csv" +PathLike = Union[str, pathlib.Path] + + +def parse_folder(source: PathLike, quiet: bool = False) -> pandas.DataFrame: + """parses an assay result folder + + The function will first try to use an assay results xml file, and will + fall back to parsing csv files if the xml file could not be parsed. + + Args: + folder: path of folder containing the assay result + quiet: skip sanity check for csv files, defaults to False + + Returns: + a pandas data frame with parsed data + """ + try: + return parse_xml_folder(source) + except ValueError: + pass + return parse_csv_folder(source, quiet) + @click.command() @click.argument( @@ -42,18 +66,22 @@ DEFAULT_OUTPUT_FILENAME = "collected_data.csv" "--quiet", is_flag=True, default=False, - help="Ignore Sanity Check", + help="Ignore sanity check for csv file parsing", ) def main(sources, output, quiet=False): """Parses the measurement results of the Sensospot reader The resulting output is either echoed to stdout or saved to a file. + At first parsing the assay result xml file is tried. + I this doesn't work, the fallback is to parse the csv files. """ paths = (pathlib.Path(source) for source in sources) - collection = (parse_csv_folder(source, quiet) for source in paths) - result = pandas.concat(collection, ignore_index=True).to_csv( - output, sep="\t", index=False + collection = (parse_folder(source, quiet) for source in paths) + result = ( + pandas.concat(collection, ignore_index=True) + .reset_index() + .to_csv(output, sep="\t", index=False) ) # if 'output' is None, the call to 'to_csv()' returns the csv as text # if 'output' is not None, 'to_csv()' writes to the file and returns None diff --git a/src/sensospot_parser/xml_parser.py b/src/sensospot_parser/xml_parser.py new file mode 100644 index 0000000..d097944 --- /dev/null +++ b/src/sensospot_parser/xml_parser.py @@ -0,0 +1,192 @@ +""" Sensospot Data Parser + +Parsing the csv result files from Sensovations Sensospot image analysis. +""" + +import pathlib +from typing import Union, Optional +from datetime import datetime + +import pandas +from defusedxml import ElementTree + +from . import columns, parameters + +PathLike = Union[str, pathlib.Path] + +RESULT_TAG_TYPES = { + "System.Int32": int, + "System.UInt32": int, + "System.Double": float, + "System.Boolean": lambda x: x.lower() == "true", +} + +DATETIME_XML_FORMAT = "%m/%d/%Y %I:%M:%S %p" + + +class ParserTarget: + """Class to parse the event stream emitted by ElementTree.XMLParser + + The methods "start()", "data()", "end()" and "close()" are defined + according to the requirements of the ElementTree.XMLParser + """ + + def __init__(self): + """initialization of the object instance""" + self.collected = [] + self._current = {} + self._data_func = None + + def start(self, tag: str, attributes: dict[str:str]) -> None: + """start of an xml tag + + The sensovation software uses sometimes the attributes of a tag to + store relevant data and sometimes the data part of the xml tree. + + This methods extracts the data from the attributes or preparse the + parsing of the data section + + Args: + tag: the name of the tag + attributes: the attributes of the tag as a dict + """ + if tag == "ScanJobResult": + self._current[columns.ANALYSIS_NAME] = attributes["ID"] + elif tag == "AssayResult": + well = attributes["ID"] + self._current[columns.WELL_NAME] = attributes["ID"] + self._current[columns.WELL_ROW] = well[0] + self._current[columns.WELL_COLUMN] = int(well[1:]) + elif tag.startswith("ChannelConfig"): + self._current[columns.EXPOSURE_ID] = int(tag[13:]) + elif tag == "Spot": + self._current[columns.POS_ID] = int(attributes["ID"]) + elif tag == "Result": + self._result_attributes_parser(attributes) + elif tag == "Timestamp": + self._data_func = self._data_timestamp_parser + elif tag == "ImageFileName": + self._data_func = self._data_image_name_parser + + def _result_attributes_parser(self, data: dict[str:str]) -> None: + """parses the attributes of the "Result" tag""" + label = data["Label"] + converter = RESULT_TAG_TYPES.get(data["Type"], str) + self._current[label] = converter(data["Value"]) + + def _data_timestamp_parser(self, data: str) -> None: + """parses the data section of a "Timestamp" tag""" + timestamp = datetime.strptime(data.strip(), DATETIME_XML_FORMAT) + self._current[columns.ANALYSIS_DATETIME] = timestamp + + def _data_image_name_parser(self, data: str) -> None: + """parses the data section of a "ImageFileName" tag""" + self._current[columns.ANALYSIS_IMAGE] = data.strip() + + def data(self, data: str) -> None: + """parses the data section of the xml tree + + The data sections in the xml tree of the sensovation software are + not often used. + + The "start()" method sets a parser for the upcoming data section and + this parser is removed after it was called. + """ + if self._data_func: + self._data_func(data) + self._data_func = None + + def end(self, tag: str) -> None: + """the end of a tag is reached + + If it is the end of a "Spot" tag, a copy of the current data is added + to the collected data property. + """ + if tag == "Spot": + spot_data = dict(self._current) + self.collected.append(spot_data) + + def closed(self) -> None: + """the end of the xml file is reached""" + pass + + +def _find_result_xml_file(folder: PathLike) -> Optional[pathlib.Path]: + """searches a results folder for the analysis xml file + + There may be multiple xml files in the folder, but only one xsl file with + the same (base) name as the xml file we are looking for. This is why we + first look for the xsl file and then derive the path from the xml file + from it. + + Args: + folder: path of folder containing data files + + Returns: + Path to xml assay result file or None if it could not be found + """ + source = pathlib.Path(folder) + files = (i for i in source.iterdir() if i.is_file()) + not_hidden = (f for f in files if not f.name.startswith(".")) + xsl_files = [f for f in not_hidden if f.suffix == ".xsl"] + if len(xsl_files) != 1: + # multiple xsl files in a folder + # this does not to be a "normal" results folder + return None + xsl_file = xsl_files[0] + xml_file = xsl_file.with_suffix(".xml") + return xml_file if xml_file.is_file() else None + + +def parse_xml_file(xml_file: PathLike) -> pandas.DataFrame: + """parses an assay result xml file into a pandas data frame + + Will raise a ValueError on a non-parsable xml file. + + Args: + xml_file: path to the xml file + + Returns: + A pandas DataFrame with the parsed data + + Raises: + ValueError if the xml file could not be parsed + """ + xml_file = pathlib.Path(xml_file) + if not xml_file.is_file(): + raise ValueError("Xml file does not exist") + + target = ParserTarget() + parser = ElementTree.DefusedXMLParser(target=target) + + try: + parser.feed(xml_file.read_text()) + except (IndexError, KeyError, ValueError, TypeError) as e: + raise ValueError("Malformed data in xml file") from e + + data_frame = pandas.DataFrame(data=target.collected).reset_index() + if data_frame.empty: + raise ValueError("Could not parse assay results xml file") + + return columns._cleanup_data_columns(data_frame) + + +def parse_xml_folder(folder: PathLike) -> pandas.DataFrame: + """parses the xml result file in a folder to one large dataframe + + Will raise an ValueError, if no sensospot data could be found in + the folder + + Args: + folder: path of folder containing data files + + Returns: + a pandas data frame with parsed data + """ + folder = pathlib.Path(folder) + xml_file = _find_result_xml_file(folder) + if xml_file is None: + raise ValueError("Could not find assay results xml file") + data_frame = parse_xml_file(xml_file) + data_frame = parameters.add_measurement_parameters(data_frame, folder) + return columns._cleanup_data_columns(data_frame) diff --git a/tests/conftest.py b/tests/conftest.py index d176031..3c575a1 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -7,8 +7,8 @@ import pytest EXAMPLE_DIR_CSV_WO_PARAMS = "csv_wo_parameters" EXAMPLE_DIR_CSV_WITH_PARAMS = "csv_with_parameters" -EXAMPLE_DIR_XML_WO_RECORD = "xml_wo_parameters" -EXAMPLE_DIR_XML_WITH_RECORD = "xml_wo_parameters" +EXAMPLE_DIR_XML_WO_PARAMS = "xml_wo_parameters" +EXAMPLE_DIR_XML_WITH_PARAMS = "xml_with_parameters" @pytest.fixture(scope="session") diff --git a/tests/test_sensospot_data.py b/tests/test_sensospot_data.py index a8a2e16..61a83a3 100644 --- a/tests/test_sensospot_data.py +++ b/tests/test_sensospot_data.py @@ -1,8 +1,50 @@ """ testing the __ini__ file """ +import pytest + +from .conftest import EXAMPLE_DIR_CSV_WO_PARAMS, EXAMPLE_DIR_XML_WO_PARAMS def test_import_api(): from sensospot_parser import main # noqa: F401 from sensospot_parser import columns # noqa: F401 - from sensospot_parser import parse_csv_file # noqa: F401 + from sensospot_parser import parse_folder # noqa: F401 from sensospot_parser import parse_csv_folder # noqa: F401 + from sensospot_parser import parse_xml_folder # noqa: F401 + + +def test_compare_xml_to_csv(example_dir): + import pandas + + from sensospot_parser import parse_csv_folder, parse_xml_folder + + folder = example_dir / EXAMPLE_DIR_XML_WO_PARAMS + + csv_df = parse_csv_folder(folder) + xml_df = parse_xml_folder(folder) + + assert isinstance(csv_df, pandas.DataFrame) + assert isinstance(xml_df, pandas.DataFrame) + + assert len(csv_df) == len(xml_df) + assert set(csv_df["Well.Name"]) == set(xml_df["Well.Name"]) + assert set(csv_df["Exposure.Id"]) == set(xml_df["Exposure.Id"]) + assert set(csv_df["Spot.Diameter"]) == set(xml_df["Spot.Diameter"]) + + +@pytest.mark.parametrize( + "folder, length, hasnans", + [ + (EXAMPLE_DIR_XML_WO_PARAMS, 6400, False), + (EXAMPLE_DIR_CSV_WO_PARAMS, 28800, True), + ], +) +def test_parse_folder_switches_parser(example_dir, folder, length, hasnans): + import pandas + + from sensospot_parser import parse_folder + + result = parse_folder(example_dir / folder) + + assert isinstance(result, pandas.DataFrame) + assert len(result) == length + assert result["Analysis.Datetime"].hasnans == hasnans diff --git a/tests/test_xml_parser.py b/tests/test_xml_parser.py new file mode 100644 index 0000000..a485ddf --- /dev/null +++ b/tests/test_xml_parser.py @@ -0,0 +1,341 @@ +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)