def test_subtract_blank(self):
res = False
with app.app_context():
la = self.get_inst_from_step('filter_expected.csv')
expected = self.csv_to_row_dict(self.sample_data_dir +
'subtract_expected.csv')
la.subtract_blank('c', form.MULT_FACTOR_DEFAULT)
res, msg = self.diff_dicts(expected, la.rows)
self.assertTrue(res, msg)
def test_normalize(self):
res = False
with app.app_context():
la = self.get_inst_from_step('remove_expected.csv')
expected = self.csv_to_row_dict(self.sample_data_dir +
'normalize_expected.csv')
la.normalize({'normalize': 'intensity'})
res, msg = self.diff_dicts(expected, la.rows)
self.assertTrue(res, msg)
def test_group_ions_diff(self):
res = False
with app.app_context():
la = self.get_inst_from_step('init_expected.csv')
expected = self.csv_to_row_dict(self.sample_data_dir +
'group_ions_expected.csv')
la.group_ions(form.ION_GROUP_WITHIN_DEFAULT)
res, msg = self.diff_dicts(expected, la.rows)
self.assertTrue(res, msg)
def test_class_stats(self):
res = False
with app.app_context():
# no normalization is the default, use remove_expected to init rows
la = self.get_inst_from_step('remove_expected.csv')
expected = self.csv_to_row_dict(
self.sample_data_dir + 'class_stats_expected.csv', 'class')
la.calc_class_stats({'class_stats': 'y'})
res, msg = self.diff_dicts(expected, la.class_dict)
self.assertTrue(res, msg)
def test_lipid_analysis_init_cnt(self):
res = False
with app.app_context():
la = LipidAnalysis([
self.sample_data_dir + 'neg_short.txt',
self.sample_data_dir + 'pos_short.txt'
])
# check that rows have expected count
res = (len(la.rows) == 64)
assert res
def test_remove_columns(self):
res = False
with app.app_context():
la = self.get_inst_from_step('subtract_expected.csv')
expected = self.csv_to_row_dict(self.sample_data_dir +
'remove_expected.csv')
la.remove_columns(', '.join(form.COLS_TO_REMOVE))
test_cols = la.rows[next(iter(la.rows))].keys()
expected_cols = expected[next(iter(expected))].keys()
same, msg = self.diff_keys(expected_cols, test_cols)
self.assertTrue(same, msg)
def test_filter_rows_default(self):
res = False
with app.app_context():
la = self.get_inst_from_step('group_ions_expected.csv')
expected = self.csv_to_row_dict(self.sample_data_dir +
'filter_expected.csv')
la.filter_rows(form.RET_TIME_DEFAULT, form.GROUP_PQ_DEFAULT,
form.GROUP_SN_DEFAULT, form.GROUP_AREA_DEFAULT,
form.GROUP_HEIGHT_DEFAULT)
res, msg = self.diff_dicts(expected, la.rows)
self.assertTrue(res, msg)
def test_lipid_analysis_init_diff(self):
res = False
with app.app_context():
la = LipidAnalysis([
self.sample_data_dir + 'neg_short.txt',
self.sample_data_dir + 'pos_short.txt'
])
expected = self.csv_to_row_dict(self.sample_data_dir +
'init_expected.csv')
res, msg = self.diff_dicts(expected, la.rows)
self.assertTrue(res, msg)