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sensospot_parser
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Changes after linting with "ruff"

master
Holger Frey 2 years ago
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commit
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10 changed files with 113 additions and 92 deletions
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  1. 8
      src/sensospot_parser/__init__.py
  2. 24
      src/sensospot_parser/csv_parser.py
  3. 13
      src/sensospot_parser/parameters.py
  4. 19
      src/sensospot_parser/xml_parser.py
  5. 20
      tests/conftest.py
  6. 1
      tests/test_columns.py
  7. 29
      tests/test_csv_parser.py
  8. 4
      tests/test_parameters.py
  9. 16
      tests/test_sensospot_data.py
  10. 71
      tests/test_xml_parser.py

8
src/sensospot_parser/__init__.py
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@ -21,7 +21,7 @@ DEFAULT_OUTPUT_FILENAME = "collected_data.csv"
PathLike = Union[str, pathlib.Path] PathLike = Union[str, pathlib.Path]
def parse_folder(source: PathLike, quiet: bool = False) -> pandas.DataFrame: def parse_folder(source: PathLike, *, quiet: bool = False) -> pandas.DataFrame:
"""parses an assay result folder """parses an assay result folder
The function will first try to use an assay results xml file, and will The function will first try to use an assay results xml file, and will
@ -38,7 +38,7 @@ def parse_folder(source: PathLike, quiet: bool = False) -> pandas.DataFrame:
return parse_xml_folder(source) return parse_xml_folder(source)
except ValueError: except ValueError:
pass pass
return parse_csv_folder(source, quiet) return parse_csv_folder(source, quiet=quiet)
@click.command() @click.command()
@ -68,7 +68,7 @@ def parse_folder(source: PathLike, quiet: bool = False) -> pandas.DataFrame:
default=False, default=False,
help="Ignore sanity check for csv file parsing", help="Ignore sanity check for csv file parsing",
) )
def main(sources, output, quiet=False): def main(sources, output, quiet=False): # noqa: FBT002
"""Parses the measurement results of the Sensospot reader """Parses the measurement results of the Sensospot reader
The resulting output is either echoed to stdout or saved to a file. The resulting output is either echoed to stdout or saved to a file.
@ -77,7 +77,7 @@ def main(sources, output, quiet=False):
I this doesn't work, the fallback is to parse the csv files. I this doesn't work, the fallback is to parse the csv files.
""" """
paths = (pathlib.Path(source) for source in sources) paths = (pathlib.Path(source) for source in sources)
collection = (parse_folder(source, quiet) for source in paths) collection = (parse_folder(source, quiet=quiet) for source in paths)
result = ( result = (
pandas.concat(collection, ignore_index=True) pandas.concat(collection, ignore_index=True)
.reset_index() .reset_index()

24
src/sensospot_parser/csv_parser.py
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@ -3,10 +3,10 @@
Parsing the csv result files from Sensovations Sensospot image analysis. Parsing the csv result files from Sensovations Sensospot image analysis.
""" """
import re
import pathlib import pathlib
from typing import Union, TextIO, Optional, Sequence import re
from collections import namedtuple from collections import namedtuple
from typing import Optional, Sequence, TextIO, Union
import pandas import pandas
@ -74,10 +74,11 @@ def _extract_measurement_info(data_file: PathLike) -> FileInfo:
named tuple FileInfo with parsed metadata named tuple FileInfo with parsed metadata
""" """
data_path = pathlib.Path(data_file) data_path = pathlib.Path(data_file)
*rest, well, exposure = data_path.stem.rsplit("_", 2) # noqa: F841 *rest, well, exposure = data_path.stem.rsplit("_", 2)
matched = REGEX_WELL.match(well) matched = REGEX_WELL.match(well)
if matched is None: if matched is None:
raise ValueError(f"not a valid well: '{well}'") msg = f"not a valid well: '{well}'"
raise ValueError(msg)
row = matched["row"].upper() row = matched["row"].upper()
column = int(matched["column"]) column = int(matched["column"])
exposure = int(exposure) exposure = int(exposure)
@ -143,7 +144,8 @@ def parse_multiple_csv_files(
pandas data frame with all parsed data combined pandas data frame with all parsed data combined
""" """
if not file_list: if not file_list:
raise ValueError("Empty file list provided") msg = "Empty file list provided"
raise ValueError(msg)
collection = (_parse_csv_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) filtered = (frame for frame in collection if frame is not None)
data_frame = pandas.concat(filtered, ignore_index=True).reset_index() data_frame = pandas.concat(filtered, ignore_index=True).reset_index()
@ -186,9 +188,8 @@ def _sanity_check(data_frame: pandas.DataFrame) -> pandas.DataFrame:
spot_positions = len(data_frame[columns.POS_ID].unique()) spot_positions = len(data_frame[columns.POS_ID].unique())
expected_rows = field_rows * field_cols * exposures * spot_positions expected_rows = field_rows * field_cols * exposures * spot_positions
if expected_rows != len(data_frame): if expected_rows != len(data_frame):
raise ValueError( msg = f"Measurements are missing: {expected_rows} != {len(data_frame)}"
f"Measurements are missing: {expected_rows} != {len(data_frame)}" raise ValueError(msg)
)
# set the right data type for measurement columns # set the right data type for measurement columns
for raw_column in columns.NUMERIC_COLUMNS: for raw_column in columns.NUMERIC_COLUMNS:
data_frame[raw_column] = pandas.to_numeric(data_frame[raw_column]) data_frame[raw_column] = pandas.to_numeric(data_frame[raw_column])
@ -196,7 +197,7 @@ def _sanity_check(data_frame: pandas.DataFrame) -> pandas.DataFrame:
def parse_csv_folder( def parse_csv_folder(
folder: PathLike, quiet: bool = False folder: PathLike, *, quiet: bool = False
) -> pandas.DataFrame: ) -> pandas.DataFrame:
"""parses all csv files in a folder to one large dataframe """parses all csv files in a folder to one large dataframe
@ -214,8 +215,9 @@ def parse_csv_folder(
file_list = find_csv_files(folder_path) file_list = find_csv_files(folder_path)
try: try:
data_frame = parse_multiple_csv_files(file_list) data_frame = parse_multiple_csv_files(file_list)
except ValueError: except ValueError as e:
raise ValueError(f"No sensospot data found in folder '{folder}'") msg = f"No sensospot data found in folder '{folder}'"
raise ValueError(msg) from e
data_frame = add_measurement_parameters(data_frame, folder_path) data_frame = add_measurement_parameters(data_frame, folder_path)

13
src/sensospot_parser/parameters.py
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@ -4,8 +4,8 @@ Parsing the numerical output from Sensovations Sensospot image analysis.
""" """
import pathlib import pathlib
from typing import Any, Dict, Union, Optional from typing import Any, Dict, Optional, Union
from xml.etree.ElementTree import Element as ElementType # noqa: S405 from xml.etree.ElementTree import Element as ElementType
import numpy import numpy
import pandas import pandas
@ -30,10 +30,7 @@ def _search_params_file(folder: PathLike) -> Optional[pathlib.Path]:
if not params_folder.is_dir(): if not params_folder.is_dir():
return None return None
param_files = list(params_folder.glob("**/*.svexp")) param_files = list(params_folder.glob("**/*.svexp"))
if len(param_files) == 1: return param_files[0] if len(param_files) == 1 else None
return param_files[0]
else:
return None
def _get_channel_data(channel_node: ElementType) -> Dict[str, Any]: def _get_channel_data(channel_node: ElementType) -> Dict[str, Any]:
@ -45,9 +42,9 @@ def _get_channel_data(channel_node: ElementType) -> Dict[str, Any]:
Returns: Returns:
dict with the information dict with the information
""" """
# child.tag == "ChannelConfig1" # Example "ChannelConfig1"
exposure_id = int(channel_node.tag[-1]) exposure_id = int(channel_node.tag[-1])
# channel_description == "[Cy3|Cy5] Green" # Example "Cy3 Green"
description = channel_node.attrib["Description"] description = channel_node.attrib["Description"]
exposure_channel = description.rsplit(" ", 1)[-1] exposure_channel = description.rsplit(" ", 1)[-1]
# floats can be used for exposure times, not only ints # floats can be used for exposure times, not only ints

19
src/sensospot_parser/xml_parser.py
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@ -4,8 +4,8 @@ Parsing the csv result files from Sensovations Sensospot image analysis.
""" """
import pathlib import pathlib
from typing import Union, Optional
from datetime import datetime from datetime import datetime
from typing import Optional, Union
import pandas import pandas
from defusedxml import ElementTree from defusedxml import ElementTree
@ -76,7 +76,9 @@ class ParserTarget:
def _data_timestamp_parser(self, data: str) -> None: def _data_timestamp_parser(self, data: str) -> None:
"""parses the data section of a "Timestamp" tag""" """parses the data section of a "Timestamp" tag"""
timestamp = datetime.strptime(data.strip(), DATETIME_XML_FORMAT) timestamp = datetime.strptime( # noqa: DTZ007
data.strip(), DATETIME_XML_FORMAT
)
self._current[columns.ANALYSIS_DATETIME] = timestamp self._current[columns.ANALYSIS_DATETIME] = timestamp
def _data_image_name_parser(self, data: str) -> None: def _data_image_name_parser(self, data: str) -> None:
@ -108,7 +110,6 @@ class ParserTarget:
def closed(self) -> None: def closed(self) -> None:
"""the end of the xml file is reached""" """the end of the xml file is reached"""
pass
def _find_result_xml_file(folder: PathLike) -> Optional[pathlib.Path]: def _find_result_xml_file(folder: PathLike) -> Optional[pathlib.Path]:
@ -154,7 +155,8 @@ def parse_xml_file(xml_file: PathLike) -> pandas.DataFrame:
""" """
xml_file = pathlib.Path(xml_file) xml_file = pathlib.Path(xml_file)
if not xml_file.is_file(): if not xml_file.is_file():
raise ValueError("Xml file does not exist") msg = "Xml file does not exist"
raise ValueError(msg)
target = ParserTarget() target = ParserTarget()
parser = ElementTree.DefusedXMLParser(target=target) parser = ElementTree.DefusedXMLParser(target=target)
@ -162,11 +164,13 @@ def parse_xml_file(xml_file: PathLike) -> pandas.DataFrame:
try: try:
parser.feed(xml_file.read_text()) parser.feed(xml_file.read_text())
except (IndexError, KeyError, ValueError, TypeError) as e: except (IndexError, KeyError, ValueError, TypeError) as e:
raise ValueError("Malformed data in xml file") from e msg = "Malformed data in xml file"
raise ValueError(msg) from e
data_frame = pandas.DataFrame(data=target.collected).reset_index() data_frame = pandas.DataFrame(data=target.collected).reset_index()
if data_frame.empty: if data_frame.empty:
raise ValueError("Could not parse assay results xml file") msg = "Could not parse assay results xml file"
raise ValueError(msg)
return columns._cleanup_data_columns(data_frame) return columns._cleanup_data_columns(data_frame)
@ -186,7 +190,8 @@ def parse_xml_folder(folder: PathLike) -> pandas.DataFrame:
folder = pathlib.Path(folder) folder = pathlib.Path(folder)
xml_file = _find_result_xml_file(folder) xml_file = _find_result_xml_file(folder)
if xml_file is None: if xml_file is None:
raise ValueError("Could not find assay results xml file") msg = "Could not find assay results xml file"
raise ValueError(msg)
data_frame = parse_xml_file(xml_file) data_frame = parse_xml_file(xml_file)
data_frame = parameters.add_measurement_parameters(data_frame, folder) data_frame = parameters.add_measurement_parameters(data_frame, folder)
return columns._cleanup_data_columns(data_frame) return columns._cleanup_data_columns(data_frame)

20
tests/conftest.py
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@ -14,23 +14,23 @@ EXAMPLE_DIR_XML_WITH_PARAMS = "xml_with_parameters"
@pytest.fixture(scope="session") @pytest.fixture(scope="session")
def example_dir(request): def example_dir(request):
root_dir = Path(request.config.rootdir) root_dir = Path(request.config.rootdir)
yield root_dir / "example_data" return root_dir / "example_data"
@pytest.fixture @pytest.fixture()
def example_file(example_dir): def example_file(example_dir):
data_dir = example_dir / EXAMPLE_DIR_CSV_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" return data_dir / "160218_SG2-013-001_Regen1_Cy3-100_1_A1_1.csv"
@pytest.fixture @pytest.fixture()
def exposure_df(): def exposure_df():
from pandas import DataFrame from pandas import DataFrame
yield DataFrame(data={"Exposure.Id": [1, 2, 3]}) return DataFrame(data={"Exposure.Id": [1, 2, 3]})
@pytest.fixture @pytest.fixture()
def normalization_data_frame(): def normalization_data_frame():
from sensospot_parser.columns import RAW_DATA_NORMALIZATION_MAP from sensospot_parser.columns import RAW_DATA_NORMALIZATION_MAP
@ -86,10 +86,10 @@ def normalization_data_frame():
data_frame = pandas.DataFrame(overflow_test_data) data_frame = pandas.DataFrame(overflow_test_data)
data_frame["Exposure.Channel"] = "Cy5" data_frame["Exposure.Channel"] = "Cy5"
for value_column in RAW_DATA_NORMALIZATION_MAP.keys(): for value_column in RAW_DATA_NORMALIZATION_MAP:
data_frame[value_column] = data_frame["Value"] data_frame[value_column] = data_frame["Value"]
yield data_frame return data_frame
@pytest.fixture(scope="session") @pytest.fixture(scope="session")
@ -106,11 +106,11 @@ def parsed_data_frame_without_params(example_dir):
return parse_csv_folder(example_dir / EXAMPLE_DIR_CSV_WO_PARAMS) return parse_csv_folder(example_dir / EXAMPLE_DIR_CSV_WO_PARAMS)
@pytest.fixture @pytest.fixture()
def data_frame_with_params(parsed_data_frame_with_params): def data_frame_with_params(parsed_data_frame_with_params):
return parsed_data_frame_with_params.copy() return parsed_data_frame_with_params.copy()
@pytest.fixture @pytest.fixture()
def data_frame_without_params(parsed_data_frame_without_params): def data_frame_without_params(parsed_data_frame_without_params):
return parsed_data_frame_without_params.copy() return parsed_data_frame_without_params.copy()

1
tests/test_columns.py
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@ -1,6 +1,5 @@
def test_cleanup_data_columns(): def test_cleanup_data_columns():
from pandas import DataFrame from pandas import DataFrame
from sensospot_parser.columns import _cleanup_data_columns from sensospot_parser.columns import _cleanup_data_columns
columns = ["Rect.", "Contour", " ID ", "Found", "Dia."] columns = ["Rect.", "Contour", " ID ", "Found", "Dia."]

29
tests/test_csv_parser.py
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@ -4,11 +4,11 @@
import numpy import numpy
import pytest import pytest
from .conftest import EXAMPLE_DIR_CSV_WO_PARAMS, EXAMPLE_DIR_CSV_WITH_PARAMS from .conftest import EXAMPLE_DIR_CSV_WITH_PARAMS, EXAMPLE_DIR_CSV_WO_PARAMS
@pytest.mark.parametrize( @pytest.mark.parametrize(
"sub_dir, file_name", ("sub_dir", "file_name"),
[ [
( (
EXAMPLE_DIR_CSV_WO_PARAMS, EXAMPLE_DIR_CSV_WO_PARAMS,
@ -65,14 +65,15 @@ def test_parse_csv_no_array(example_dir):
@pytest.mark.parametrize( @pytest.mark.parametrize(
"input, expected", [("", "."), ("..,", "."), (".,,", ","), ("..,,", ".")] ("provided", "expected"),
[("", "."), ("..,", "."), (".,,", ","), ("..,,", ".")],
) )
def test_guess_decimal_separator_returns_correct_separator(input, expected): def test_guess_decimal_separator_returns_correct_separator(provided, expected):
from io import StringIO from io import StringIO
from sensospot_parser.csv_parser import _guess_decimal_separator from sensospot_parser.csv_parser import _guess_decimal_separator
handle = StringIO(f"header\n{input}\n") handle = StringIO(f"header\n{provided}\n")
result = _guess_decimal_separator(handle) result = _guess_decimal_separator(handle)
assert result == expected assert result == expected
@ -98,17 +99,17 @@ def test_well_regex_ok():
assert result["column"] == "123" assert result["column"] == "123"
@pytest.mark.parametrize("input", ["", "A", "1", "1A", "-1", "A-"]) @pytest.mark.parametrize("provided", ["", "A", "1", "1A", "-1", "A-"])
def test_well_regex_no_match(input): def test_well_regex_no_match(provided):
from sensospot_parser.csv_parser import REGEX_WELL from sensospot_parser.csv_parser import REGEX_WELL
result = REGEX_WELL.match(input) result = REGEX_WELL.match(provided)
assert result is None assert result is None
@pytest.mark.parametrize( @pytest.mark.parametrize(
"filename, expected", ("filename", "expected"),
[("A1_1.csv", ("A", 1, 1)), ("test/measurement_1_H12_2", ("H", 12, 2))], [("A1_1.csv", ("A", 1, 1)), ("test/measurement_1_H12_2", ("H", 12, 2))],
) )
def test_extract_measurement_info_ok(filename, expected): def test_extract_measurement_info_ok(filename, expected):
@ -123,7 +124,7 @@ def test_extract_measurement_info_ok(filename, expected):
def test_extract_measurement_info_raises_error(filename): def test_extract_measurement_info_raises_error(filename):
from sensospot_parser.csv_parser import _extract_measurement_info from sensospot_parser.csv_parser import _extract_measurement_info
with pytest.raises(ValueError): with pytest.raises(ValueError): # noqa: PT011
_extract_measurement_info(filename) _extract_measurement_info(filename)
@ -178,7 +179,7 @@ def test_parse_file_raises_error(example_dir):
/ "should_raise_value_error.csv" / "should_raise_value_error.csv"
) )
with pytest.raises(ValueError): with pytest.raises(ValueError): # noqa: PT011
parse_csv_file(csv_file) parse_csv_file(csv_file)
@ -223,7 +224,6 @@ def testparse_multiple_files_ok(example_dir, file_list):
files = [sub_dir / file for file in file_list] files = [sub_dir / file for file in file_list]
data_frame = parse_multiple_csv_files(files) data_frame = parse_multiple_csv_files(files)
print(data_frame["Exposure.Id"].unique())
assert len(data_frame) == 100 * len(files) assert len(data_frame) == 100 * len(files)
assert len(data_frame["Exposure.Id"].unique()) == len(files) assert len(data_frame["Exposure.Id"].unique()) == len(files)
@ -232,7 +232,7 @@ def testparse_multiple_files_ok(example_dir, file_list):
def testparse_multiple_files_empty_file_list(): def testparse_multiple_files_empty_file_list():
from sensospot_parser.csv_parser import parse_multiple_csv_files from sensospot_parser.csv_parser import parse_multiple_csv_files
with pytest.raises(ValueError): with pytest.raises(ValueError): # noqa: PT011
parse_multiple_csv_files([]) parse_multiple_csv_files([])
@ -242,7 +242,6 @@ def testparse_multiple_files_empty_array(example_dir):
files = [example_dir / "no_array_A1_1.csv"] files = [example_dir / "no_array_A1_1.csv"]
data_frame = parse_multiple_csv_files(files) data_frame = parse_multiple_csv_files(files)
print(data_frame["Exposure.Id"].unique())
assert len(data_frame) == 1 assert len(data_frame) == 1
@ -306,5 +305,5 @@ def test_sanity_check_raises_value_error(example_dir):
data_frame = parse_multiple_csv_files(files) data_frame = parse_multiple_csv_files(files)
data_frame = data_frame.drop(data_frame.index[1]) data_frame = data_frame.drop(data_frame.index[1])
with pytest.raises(ValueError): with pytest.raises(ValueError): # noqa: PT011
_sanity_check(data_frame) _sanity_check(data_frame)

4
tests/test_parameters.py
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@ -1,6 +1,6 @@
import pandas import pandas
from .conftest import EXAMPLE_DIR_CSV_WO_PARAMS, EXAMPLE_DIR_CSV_WITH_PARAMS from .conftest import EXAMPLE_DIR_CSV_WITH_PARAMS, EXAMPLE_DIR_CSV_WO_PARAMS
def test_search_params_file_ok(example_dir): def test_search_params_file_ok(example_dir):
@ -32,8 +32,8 @@ def test_ssearch_measurement_params_file_parameters_file(tmpdir):
def test_parse_channel_info(example_dir): def test_parse_channel_info(example_dir):
from sensospot_parser.parameters import ( from sensospot_parser.parameters import (
_search_params_file,
_parse_measurement_params, _parse_measurement_params,
_search_params_file,
) )
params = _search_params_file(example_dir / EXAMPLE_DIR_CSV_WITH_PARAMS) params = _search_params_file(example_dir / EXAMPLE_DIR_CSV_WITH_PARAMS)

16
tests/test_sensospot_data.py
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@ -5,16 +5,17 @@ from .conftest import EXAMPLE_DIR_CSV_WO_PARAMS, EXAMPLE_DIR_XML_WO_PARAMS
def test_import_api(): def test_import_api():
from sensospot_parser import main # noqa: F401 from sensospot_parser import (
from sensospot_parser import columns # noqa: F401 columns, # noqa: F401
from sensospot_parser import parse_folder # noqa: F401 main, # noqa: F401
from sensospot_parser import parse_csv_folder # noqa: F401 parse_csv_folder, # noqa: F401
from sensospot_parser import parse_xml_folder # noqa: F401 parse_folder, # noqa: F401
parse_xml_folder, # noqa: F401
)
def test_compare_xml_to_csv(example_dir): def test_compare_xml_to_csv(example_dir):
import pandas import pandas
from sensospot_parser import parse_csv_folder, parse_xml_folder from sensospot_parser import parse_csv_folder, parse_xml_folder
folder = example_dir / EXAMPLE_DIR_XML_WO_PARAMS folder = example_dir / EXAMPLE_DIR_XML_WO_PARAMS
@ -33,7 +34,7 @@ def test_compare_xml_to_csv(example_dir):
@pytest.mark.parametrize( @pytest.mark.parametrize(
"folder, length, hasnans", ("folder", "length", "hasnans"),
[ [
(EXAMPLE_DIR_XML_WO_PARAMS, 6400, False), (EXAMPLE_DIR_XML_WO_PARAMS, 6400, False),
(EXAMPLE_DIR_CSV_WO_PARAMS, 28800, True), (EXAMPLE_DIR_CSV_WO_PARAMS, 28800, True),
@ -41,7 +42,6 @@ def test_compare_xml_to_csv(example_dir):
) )
def test_parse_folder_switches_parser(example_dir, folder, length, hasnans): def test_parse_folder_switches_parser(example_dir, folder, length, hasnans):
import pandas import pandas
from sensospot_parser import parse_folder from sensospot_parser import parse_folder
result = parse_folder(example_dir / folder) result = parse_folder(example_dir / folder)

71
tests/test_xml_parser.py
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@ -2,7 +2,7 @@ from datetime import datetime
import pytest import pytest
from .conftest import EXAMPLE_DIR_XML_WO_PARAMS, EXAMPLE_DIR_XML_WITH_PARAMS from .conftest import EXAMPLE_DIR_XML_WITH_PARAMS, EXAMPLE_DIR_XML_WO_PARAMS
class DummyDataFunc: class DummyDataFunc:
@ -28,7 +28,7 @@ def test_parser_target_init():
@pytest.mark.parametrize( @pytest.mark.parametrize(
"tag, attributes, expected", ("tag", "attributes", "expected"),
[ [
("UnknownTag", {"ID": "something"}, {}), ("UnknownTag", {"ID": "something"}, {}),
( (
@ -84,7 +84,7 @@ def test_parser_target_start_image_file_name():
@pytest.mark.parametrize( @pytest.mark.parametrize(
"data_type, value, expected", ("data_type", "value", "expected"),
[ [
("unknown type", 1, "1"), ("unknown type", 1, "1"),
("System.Int32", "12", 12), ("System.Int32", "12", 12),
@ -108,16 +108,40 @@ def test_parser_target_result_attributes_parser(data_type, value, expected):
@pytest.mark.parametrize( @pytest.mark.parametrize(
"value, expected", ("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)), "3/7/2022 5:31:47 PM",
("3/07/2022 5:31:47 PM", datetime(2022, 3, 7, 17, 31, 47)), datetime(2022, 3, 7, 17, 31, 47), # noqa: DTZ001
("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)), "03/7/2022 5:31:47 PM",
("3/7/2022 5:31:47 pm", datetime(2022, 3, 7, 17, 31, 47)), datetime(2022, 3, 7, 17, 31, 47), # noqa: DTZ001
("3/7/2022 5:31:47 AM", datetime(2022, 3, 7, 5, 31, 47)), ),
(
"3/07/2022 5:31:47 PM",
datetime(2022, 3, 7, 17, 31, 47), # noqa: DTZ001
),
(
"03/07/2022 5:31:47 PM",
datetime(2022, 3, 7, 17, 31, 47), # noqa: DTZ001
),
(
"3/7/2022 5:3:47 PM",
datetime(2022, 3, 7, 17, 3, 47), # noqa: DTZ001
),
(
"3/7/2022 5:31:4 PM",
datetime(2022, 3, 7, 17, 31, 4), # noqa: DTZ001
),
(
"3/7/2022 5:31:47 pm",
datetime(2022, 3, 7, 17, 31, 47), # noqa: DTZ001
),
(
"3/7/2022 5:31:47 AM",
datetime(2022, 3, 7, 5, 31, 47), # noqa: DTZ001
),
], ],
) )
def test_parser_target_data_timestamp_parser(value, expected): def test_parser_target_data_timestamp_parser(value, expected):
@ -203,8 +227,6 @@ def test_find_result_xml_file_ok(tmp_path):
xml_file = tmp_path / "result.xml" xml_file = tmp_path / "result.xml"
xml_file.touch() xml_file.touch()
print(list(tmp_path.iterdir()))
result = _find_result_xml_file(tmp_path) result = _find_result_xml_file(tmp_path)
assert result == xml_file assert result == xml_file
@ -257,8 +279,6 @@ def test_find_result_hidden_xsl_file(tmp_path):
xml_file = tmp_path / ".result.xml" xml_file = tmp_path / ".result.xml"
xml_file.touch() xml_file.touch()
print(list(tmp_path.iterdir()))
result = _find_result_xml_file(tmp_path) result = _find_result_xml_file(tmp_path)
assert result is None assert result is None
@ -266,10 +286,9 @@ def test_find_result_hidden_xsl_file(tmp_path):
def test_parse_xml_file_ok(example_dir): def test_parse_xml_file_ok(example_dir):
import pandas import pandas
from sensospot_parser.xml_parser import ( from sensospot_parser.xml_parser import (
parse_xml_file,
_find_result_xml_file, _find_result_xml_file,
parse_xml_file,
) )
folder = example_dir / EXAMPLE_DIR_XML_WO_PARAMS folder = example_dir / EXAMPLE_DIR_XML_WO_PARAMS
@ -288,10 +307,10 @@ def test_parse_xml_file_ok(example_dir):
@pytest.mark.parametrize( @pytest.mark.parametrize(
"file_name, message", ("file_name", "message"),
[ [
("not_existing.xml", "Xml file does not exist"), ("not_existing.xml", "Xml file does not exist"),
("incomplete.xml", "Could not parse assay results xml file"), ("defect.xml", "Could not parse assay results xml file"),
("malformed_data.xml", "Malformed data in xml file"), ("malformed_data.xml", "Malformed data in xml file"),
], ],
) )
@ -300,14 +319,14 @@ def test_parse_xml_file_raies_error(file_name, message, example_dir):
xml_file = example_dir / file_name xml_file = example_dir / file_name
with pytest.raises(ValueError) as e: with pytest.raises(ValueError) as e: # noqa: PT011
parse_xml_file(xml_file) parse_xml_file(xml_file)
assert message in str(e)
assert message in str(e)
def test_parse_xml_folder_with_params(example_dir): def test_parse_xml_folder_with_params(example_dir):
import pandas import pandas
from sensospot_parser.xml_parser import parse_xml_folder from sensospot_parser.xml_parser import parse_xml_folder
folder = example_dir / EXAMPLE_DIR_XML_WITH_PARAMS folder = example_dir / EXAMPLE_DIR_XML_WITH_PARAMS
@ -321,7 +340,6 @@ def test_parse_xml_folder_with_params(example_dir):
def test_parse_xml_folder_without_params(example_dir): def test_parse_xml_folder_without_params(example_dir):
import pandas import pandas
from sensospot_parser.xml_parser import parse_xml_folder from sensospot_parser.xml_parser import parse_xml_folder
folder = example_dir / EXAMPLE_DIR_XML_WO_PARAMS folder = example_dir / EXAMPLE_DIR_XML_WO_PARAMS
@ -336,6 +354,7 @@ def test_parse_xml_folder_without_params(example_dir):
def test_parse_xml_folder_non_existing_xml_file(tmp_path): def test_parse_xml_folder_non_existing_xml_file(tmp_path):
from sensospot_parser.xml_parser import parse_xml_folder from sensospot_parser.xml_parser import parse_xml_folder
with pytest.raises(ValueError) as e: with pytest.raises(ValueError) as e: # noqa: PT011
parse_xml_folder(tmp_path) parse_xml_folder(tmp_path)
assert "Could not find assay results xml file" in str(e)
assert "Could not find assay results xml file" in str(e)

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