def test_volatility_invalid_columns(self):
with self.assertRaisesRegex(ValueError, "peanut is not a column"):
volatility(
output_dir=self.temp_dir.name, metadata=self.md_ecam_fp,
metric='observed_otus', group_column='peanut',
state_column='month', individual_id_column='studyid',
spaghetti='yes')
def test_volatility_invalid_metric(self):
with self.assertRaisesRegex(ValueError, "metric must be a valid"):
volatility(
output_dir=self.temp_dir.name, metadata=self.md_ecam_fp,
metric='peanut', group_column='delivery',
state_column='month', individual_id_column='studyid',
spaghetti='yes')
def test_volatility_numeric_group_column(self):
with self.assertRaisesRegex(ValueError, 'observed_otu.*not a column'):
volatility(
output_dir=self.temp_dir.name, metadata=self.md_ecam_fp,
default_metric='observed_otus',
default_group_column='observed_otus', state_column='month',
individual_id_column='studyid')
def test_volatility_must_use_unique_columns(self):
with self.assertRaisesRegex(ValueError, "set to unique values"):
volatility(
output_dir=self.temp_dir.name, metadata=self.md_ecam_fp,
metric='observed_otus', group_column='studyid',
state_column='month', individual_id_column='studyid',
spaghetti='yes')
def test_volatility_categorical_state_column(self):
with self.assertRaisesRegex(TypeError, 'must be numeric'):
volatility(
output_dir=self.temp_dir.name, metadata=self.md_ecam_fp,
default_metric='observed_otus',
default_group_column='delivery', state_column='delivery',
individual_id_column='studyid')
def test_volatility_metric_and_group(self):
# Just a simple "does it run?" test. Not much worth testing in terms
# of the rendered output - vega does all the heavy lifting for us.
volatility(
output_dir=self.temp_dir.name, metadata=self.md_ecam_fp,
default_metric='observed_otus', default_group_column='delivery',
state_column='month', individual_id_column='studyid')
def test_volatility(self):
volatility(output_dir=self.temp_dir.name,
metadata=self.md_ecam_fp,
metric='observed_otus',
group_column='delivery',
state_column='month',
individual_id_column='studyid')
def test_volatility_categorical_metric_column(self):
with self.assertRaisesRegex(ValueError, 'delivery.*not a column'):
volatility(output_dir=self.temp_dir.name,
metadata=self.md_ecam_fp,
default_metric='delivery',
default_group_column='delivery',
state_column='month',
individual_id_column='studyid')
def test_volatility_invalid_metric(self):
with self.assertRaisesRegex(ValueError, "'peanut' is not a column"):
volatility(output_dir=self.temp_dir.name,
metadata=self.md_ecam_fp,
default_metric='peanut',
default_group_column='delivery',
state_column='month',
individual_id_column='studyid')
def test_volatility_table(self):
volatility(output_dir=self.temp_dir.name,
metadata=self.md_ecam_fp,
default_metric='e2c3ff4f647112723741aa72087f1bfa',
default_group_column='delivery',
state_column='month',
individual_id_column='studyid',
table=self.table_ecam_fp)
def test_volatility_no_individual_id_column(self):
# Just a simple "does it run?" test.
# plus make sure spaghetti maker is turned off.
volatility(output_dir=self.temp_dir.name,
metadata=self.md_ecam_fp,
state_column='month')
html_path = os.path.join(self.temp_dir.name, 'index.html')
with open(html_path, 'r') as f:
f = f.read()
self.assertNotIn('"spaghettis"', f)
def test_volatility_single_state(self):
single_state = self.md_ecam_fp.to_dataframe()
single_state = single_state[single_state['month'] == 0]
# state_column must contain at least two unique values...
with self.assertRaisesRegex(ValueError, "state_column must contain"):
volatility(
output_dir=self.temp_dir.name,
metadata=qiime2.Metadata(single_state),
metric='observed_otus', group_column='delivery',
state_column='month', individual_id_column='studyid',
spaghetti='yes')
def test_volatility(self):
# Simultaneously "does it run" viz test
# plus make sure spaghetti maker works
volatility(
output_dir=self.temp_dir.name, metadata=self.md_ecam_fp,
state_column='month', individual_id_column='studyid')
html_path = os.path.join(self.temp_dir.name, 'index.html')
with open(html_path, 'r') as f:
f = f.read()
self.assertIn('"spaghettis"', f)
self.assertIn('spaghettiLineThickness', f)
self.assertIn('spaghettiLineOpacity', f)
self.assertIn('spaghettiSymbolSize', f)
self.assertIn('spaghettiSymbolOpacity', f)
self.assertIn('#spaghetti-line-thickness', f)
self.assertIn('#spaghetti-line-opacity', f)
self.assertIn('#spaghetti-symbol-size', f)
self.assertIn('#spaghetti-symbol-opacity', f)
def test_volatility_no_spaghetti_no_control(self):
volatility(
output_dir=self.temp_dir.name, metadata=self.md_ecam_fp,
metric='observed_otus', group_column='delivery',
state_column='month', individual_id_column='studyid',
spaghetti='no', plot_control_limits=False)
