def adaptor_check(test_dict):
list_of_row_dicts = read_xlsx_file(test_dict["input"])
results = {"molecules": list()}
for row_dict in list_of_row_dicts:
results["molecules"].append(row_dict["molecule"])
assert len(results["molecules"]) == len(test_dict["output"]["molecules"])
def adaptor_check(test_dict):
list_of_row_dicts = read_xlsx_file(test_dict['input'])
results = {'molecules': list()}
for row_dict in list_of_row_dicts:
results['molecules'].append(row_dict['molecule'])
assert len(results['molecules']) == len(test_dict['output']['molecules'])
def quant_summary_test(self):
results_class = pickle.load(
open(os.path.join("tests", "data", "test_BSA_pyqms_results.pkl"),
"rb"))
quant_summary_collector = []
for pos, file_extension in enumerate(
["xlsx", "csv", "extension_unknown"]):
quant_summary_file = os.path.join(
"tests", "data",
"test_quant_summary.{0}".format(file_extension))
if pos == 2:
with self.assertRaises(SystemExit) as system_exit_check:
results_class.calc_amounts_from_rt_info_file(
rt_info_file=quant_summary_file,
rt_border_tolerance=None)
self.assertEqual(system_exit_check.exception.code, 1)
else:
# test csv writing
results_class.write_rt_info_file(
output_file=quant_summary_file,
rt_border_tolerance=1,
update=True)
assert os.path.exists(quant_summary_file) is True
results_class.calc_amounts_from_rt_info_file(
rt_info_file=quant_summary_file,
rt_border_tolerance=1,
calc_amount_function=None,
)
if file_extension == "csv":
read_in_line_dicts = []
for line_dict in csv.DictReader(
open(quant_summary_file, "r")):
read_in_line_dicts.append(line_dict)
else:
read_in_line_dicts = read_xlsx_file(quant_summary_file)
for line_dict in read_in_line_dicts:
assert line_dict["max I in window"] != ""
assert line_dict["max I in window (rt)"] != ""
assert line_dict["max I in window (score)"] != ""
assert len(read_in_line_dicts) == len(results_class.keys())
quant_summary_collector.append(read_in_line_dicts)
assert len(quant_summary_collector[0]) == len(
quant_summary_collector[1])
return