def test_validate_input_values(self):
# should not raise error
_validate_input_columns(md, "ind", "Group", "Time", None)
_validate_input_columns(md, "ind", None, None, None)
_validate_input_values(md, "Value", "ind", "Group", "Time", None, None)
with self.assertRaisesRegex(ValueError, "state_1 and state_2"):
_validate_input_values(md, "Value", "ind", "Group", "Time", 1, 1)
with self.assertRaisesRegex(ValueError, "not present"):
_validate_input_values(md, "Value", "ind", "Group", "Time", 1, 3)
with self.assertRaisesRegex(ValueError, "not a column"):
_validate_input_values(md, "Value", "ind", "Group", "Days", 1, 2)
with self.assertRaisesRegex(ValueError, "not a column"):
_validate_input_columns(md, "ind", ["Group", "More stuff"], "Time",
"Value")
with self.assertRaisesRegex(ValueError, "unique values"):
_validate_input_columns(md, "ind", "Time", "Time", "Value")
with self.assertRaisesRegex(ValueError, "state_column must contain"):
_validate_input_columns(
md[md['Time'] == 1], "ind", "Group", "Time", "Value")
dropped = md.drop(['9', '10', '11'])
with self.assertRaisesRegex(ValueError, "not represented"):
_validate_input_values(
dropped, "Value", "ind", "Group", "Time", 1, 2)
with self.assertRaisesRegex(ValueError, "state_1 and state_2"):
pairwise_differences(
output_dir=self.temp_dir.name, table=None,
metadata=self.md_ecam_fp, group_column='delivery',
state_column='month', state_1=0, state_2=0,
individual_id_column='studyid', metric='observed_otus',
replicate_handling='drop')
with self.assertRaisesRegex(ValueError, "Detected replicate samples"):
_get_group_pairs(
md_dup, 'a', individual_id_column='ind', group_column='Group',
state_column='Time', state_values=[1, 2],
replicate_handling='error')
def test_pairwise_differences(self):
pairwise_differences(
output_dir=self.temp_dir.name, table=None,
metadata=self.md_ecam_fp, group_column='delivery',
state_column='month', state_1=0, state_2=3,
individual_id_column='studyid', metric='observed_otus',
replicate_handling='drop')
def test_pairwise_differences_taxa(self):
pairwise_differences(
output_dir=self.temp_dir.name, table=self.table_ecam_fp,
metadata=self.md_ecam_fp, group_column='delivery',
state_column='month', state_1=0, state_2=3,
individual_id_column='studyid',
metric='e2c3ff4f647112723741aa72087f1bfa',
replicate_handling='drop')
def test_validate_input_values(self):
with self.assertRaisesRegex(ValueError, "state_1 and state_2"):
_validate_input_values(md, "ind", "Group", "Time", 1, 1)
with self.assertRaisesRegex(ValueError, "not present"):
_validate_input_values(md, "ind", "Group", "Time", 1, 3)
with self.assertRaisesRegex(ValueError, "not a column"):
_validate_input_values(md, "ind", "Group", "Days", 1, 2)
with self.assertRaisesRegex(ValueError, "not a column"):
_validate_input_columns(md, "ind", ["Group", "More stuff"], "Time")
dropped = md.drop(['9', '10', '11'])
with self.assertRaisesRegex(ValueError, "not represented"):
_validate_input_values(dropped, "ind", "Group", "Time", 1, 2)
with self.assertRaisesRegex(ValueError, "state_1 and state_2"):
pairwise_differences(
output_dir=self.temp_dir.name, table=None,
metadata=self.md_ecam_fp, group_column='delivery',
state_column='month', state_1=0, state_2=0,
individual_id_column='studyid', metric='observed_otus',
replicate_handling='drop')
