def setUp(self):
self.tstr = '(((((feature-2)e)d,feature-1)c)b)a;'
self.obj = GroupTaxonomy(name='sample-2',
taxonomy=self.tstr,
features=['feature-1', 'feature-2'],
feature_values=[1. / 5, 4. / 5],
feature_variances=[0.0, 0.0])
class GroupTaxonomyTests(unittest.TestCase):
def setUp(self):
self.tstr = '(((((feature-2)e)d,feature-1)c)b)a;'
self.obj = GroupTaxonomy(name='sample-2',
taxonomy=self.tstr,
features=['feature-1', 'feature-2'],
feature_values=[1. / 5, 4. / 5],
feature_variances=[0.0, 0.0])
def test_init(self):
self.assertEqual(self.obj.name, 'sample-2')
self.assertEqual(self.obj.taxonomy, self.tstr)
self.assertEqual(self.obj.features, ['feature-1', 'feature-2'])
self.assertEqual(self.obj.feature_values, [1. / 5, 4. / 5])
self.assertEqual(self.obj.feature_variances, [0.0, 0.0])
def test_init_tree_missing_feature(self):
with self.assertRaisesRegex(UnknownID, "is not in the taxonomy."):
GroupTaxonomy(name='sample-2',
taxonomy=self.tstr,
features=['feature-1', 'feature-3'],
feature_values=[1. / 5, 4. / 5],
feature_variances=[0.0, 0.0])
def test_init_feature_value_lengths(self):
with self.assertRaisesRegex(ValueError, "length mismatch"):
GroupTaxonomy(name='sample-2',
taxonomy=self.tstr + 'feature-3',
features=['feature-1', 'feature-2', 'feature-3'],
feature_values=[1. / 5, 4. / 5],
feature_variances=[0.0, 0.0])
with self.assertRaisesRegex(ValueError, "length mismatch"):
GroupTaxonomy(name='sample-2',
taxonomy=self.tstr,
features=['feature-1', 'feature-2'],
feature_values=[
1. / 5,
],
feature_variances=[0.0, 0.0])
def test_to_dict(self):
exp = {
'name': 'sample-2',
'taxonomy': self.tstr,
'features': ['feature-1', 'feature-2'],
'feature_values': [1. / 5, 4. / 5],
'feature_variances': [0.0, 0.0]
}
obs = self.obj.to_dict()
self.assertEqual(obs, exp)
def test_str(self):
exp = str(self.obj.to_dict())
obs = str(self.obj)
self.assertEqual(obs, exp)
def test_init_feature_value_lengths(self):
with self.assertRaisesRegex(ValueError, "length mismatch"):
GroupTaxonomy(name='sample-2',
taxonomy=self.tstr + 'feature-3',
features=['feature-1', 'feature-2', 'feature-3'],
feature_values=[1. / 5, 4. / 5],
feature_variances=[0.0, 0.0])
with self.assertRaisesRegex(ValueError, "length mismatch"):
GroupTaxonomy(name='sample-2',
taxonomy=self.tstr,
features=['feature-1', 'feature-2'],
feature_values=[
1. / 5,
],
feature_variances=[0.0, 0.0])
def test_init_tree_missing_feature(self):
with self.assertRaisesRegex(UnknownID, "is not in the taxonomy."):
GroupTaxonomy(name='sample-2',
taxonomy=self.tstr,
features=['feature-1', 'feature-3'],
feature_values=[1. / 5, 4. / 5],
feature_variances=[0.0, 0.0])
def test_get_group(self):
taxonomy = Taxonomy(self.table, self.taxonomy_df)
exp = GroupTaxonomy(name='sample-2',
taxonomy='((((feature-1,((feature-2)e)d)c)b)a);',
features=['feature-1', 'feature-2'],
feature_values=[1. / 5, 4. / 5],
feature_variances=[0.0, 0.0])
obs = taxonomy.get_group(['sample-2'])
self.assertEqual(obs, exp)
def test_get_group_with_variances(self):
taxonomy = Taxonomy(self.table, self.taxonomy_df, self.table_vars)
exp = GroupTaxonomy(
name='sample-1',
taxonomy='((((((feature-2)e)d)c)b,(((feature-3)h)g)f)a);', # noqa
features=['feature-2', 'feature-3'],
feature_values=[2. / 5, 3. / 5],
feature_variances=[2.0, 3.0])
obs = taxonomy.get_group(['sample-1'])
self.assertEqual(obs, exp)
def test_get_group_multiple(self):
taxonomy = Taxonomy(self.table, self.taxonomy_df)
exp = GroupTaxonomy(
name='foo',
taxonomy=
'((((feature-1,((feature-2)e)d)c)b,(((feature-3)h)g)f)a);', # noqa
features=['feature-1', 'feature-2', 'feature-3'],
feature_values=[1. / 10, 6. / 10, 3. / 10],
feature_variances=[0.0, 0.0, 0.0])
obs = taxonomy.get_group(['sample-1', 'sample-2'], 'foo')
self.assertEqual(obs.name, exp.name)
self.assertEqual(obs.taxonomy, exp.taxonomy)
self.assertEqual(obs.features, exp.features)
npt.assert_almost_equal(obs.feature_values, exp.feature_values)
self.assertEqual(obs.feature_variances, exp.feature_variances)