def test_taxonomy_from_list_unknown_sample(self):
# NOTE: do not delete this test when converting _alt methods to non
# _alt methods
# One ID not found (out of two)
with patch.object(TaxonomyRepo, 'exists') as mock_exists, \
patch.object(TaxonomyRepo, 'resources') as mock_resources:
mock_resources.return_value = ['foo-table']
mock_exists.side_effect = [True, False]
response, code = _summarize_group(
['sample-1', 'sample-baz-bat'],
'foo-table',
taxonomy_repo=TaxonomyRepo(),
)
api_out = json.loads(response.data)
self.assertListEqual(api_out['missing_ids'], ['sample-baz-bat'])
self.assertRegex(api_out['text'], r'Sample ID\(s\) not found.')
self.assertEqual(code, 404)
# Multiple IDs do not exist
with patch.object(TaxonomyRepo, 'exists') as mock_exists, \
patch.object(TaxonomyRepo, 'resources') as mock_metrics:
mock_metrics.return_value = ['bar-table']
mock_exists.side_effect = [False, False]
response, code = _summarize_group(
['sample-foo-bar', 'sample-baz-bat'],
'bar-table',
taxonomy_repo=TaxonomyRepo(),
)
api_out = json.loads(response.data)
self.assertListEqual(api_out['missing_ids'],
['sample-foo-bar', 'sample-baz-bat'])
self.assertRegex(api_out['text'], r'Sample ID\(s\) not found.')
self.assertEqual(code, 404)
def test_taxonomy_from_list_summarize_group_one_sample_with_variance(self):
# NOTE: do not delete this test when converting _alt methods to non
# _alt methods
with patch(
'microsetta_public_api.repo._taxonomy_repo.TaxonomyRepo.'
'tables',
new_callable=PropertyMock) as mock_tables:
mock_tables.return_value = {
'some-table': {
'table': self.table,
'feature-data-taxonomy': self.taxonomy_df,
'variances': self.table_vars,
},
}
response, code = _summarize_group(
['sample-1'],
"some-table",
taxonomy_repo=TaxonomyRepo(),
)
self.assertEqual(code, 200)
exp_keys = [
'taxonomy', 'features', 'feature_values', 'feature_variances'
]
obs = json.loads(response)
self.assertCountEqual(exp_keys, obs.keys())
self.assertEqual('((((((feature-2)e)d)c)b,(((feature-3)h)g)f)a);',
obs['taxonomy'])
self.assertListEqual(['feature-2', 'feature-3'], obs['features'])
assert_allclose([2. / 5, 3. / 5], obs['feature_values'])
assert_allclose([2.0, 3.0], obs['feature_variances'])
def test_taxonomy_from_list_summarize_group_simple_with_variances(self):
with patch(
'microsetta_public_api.repo._taxonomy_repo.TaxonomyRepo.'
'tables',
new_callable=PropertyMock) as mock_tables:
mock_tables.return_value = {
'some-table': {
'table': self.table,
'feature-data-taxonomy': self.taxonomy_df,
'variances': self.table_vars,
},
}
response, code = _summarize_group(self.post_body['sample_ids'],
"some-table")
self.assertEqual(code, 200)
exp_keys = [
'taxonomy', 'features', 'feature_values', 'feature_variances'
]
obs = json.loads(response)
self.assertCountEqual(exp_keys, obs.keys())
self.assertEqual(
'((((feature-1,((feature-2)e)d)c)b,'
'(((feature-3)h)g)f)a);', obs['taxonomy'])
self.assertListEqual(['feature-1', 'feature-2', 'feature-3'],
obs['features'])
assert_allclose([1. / 10, 6. / 10, 3. / 10], obs['feature_values'])
assert_allclose([0, 0, 0], obs['feature_variances'])
def test_taxonomy_from_list_unknown_resource(self):
with patch.object(TaxonomyRepo, 'resources') as mock_resources:
mock_resources.return_value = ['alpha', 'beta']
response, code = _summarize_group(list(self.post_body.values()),
'some-other-table')
api_out = json.loads(response.data)
self.assertRegex(
api_out['text'], r"Requested resource: 'some-other-table' is "
r"unavailable. "
r"Available resource\(s\): \[(.*)\]")
self.assertEqual(code, 404)