def test_taxonomy_from_list_summarize_group_simple_cached_model(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,
'model': TaxonomyModel(self.table, self.taxonomy_df)
},
}
response, code = _summarize_group(
self.post_body['sample_ids'],
"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-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 _get_taxonomy_repo(dataset):
tables = stepwise_resource_getter(
get_resources(),
dataset,
schema.taxonomy_kw,
'taxonomy',
)
taxonomy_repo = TaxonomyRepo(tables.data)
return taxonomy_repo
def test_get_resource_component(self):
taxonomy_repo = TaxonomyRepo()
with patch(
'microsetta_public_api.repo._taxonomy_repo.TaxonomyRepo'
'.tables',
new_callable=PropertyMock) as mock_tables:
mock_tables.return_value = {
'foo': {
'table': 'some-tb',
'variances': 'var-tb'
},
'bar': {
'table': 'some-other-tb'
}
}
res = taxonomy_repo._get_resource('bar')
self.assertDictEqual({'table': 'some-other-tb'}, res)
def test_get_resource_table_not_available(self):
taxonomy_repo = TaxonomyRepo()
with patch(
'microsetta_public_api.repo._taxonomy_repo.TaxonomyRepo'
'.tables',
new_callable=PropertyMock) as mock_tables:
mock_tables.return_value = {
'foo': {
'table': 'some-tb'
},
'bar': {
'table': 'some-other-tb'
}
}
with self.assertRaisesRegex(
ValueError, 'No table with taxonomy '
'available for '
'`bad-table`'):
taxonomy_repo._get_resource('bad-table')
def test_taxonomy_from_list_unknown_resource(self):
# NOTE: do not delete this test when converting _alt methods to non
# _alt methods
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',
taxonomy_repo=TaxonomyRepo(),
)
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)
def summarize_group(body, resource):
sample_ids = body['sample_ids']
taxonomy_repo = TaxonomyRepo()
return _summarize_group(sample_ids, resource, taxonomy_repo)
def single_sample(sample_id, resource):
sample_ids = [sample_id]
taxonomy_repo = TaxonomyRepo()
return _summarize_group(sample_ids, resource, taxonomy_repo)
def exists_group(body, resource):
return _exists(resource, body, taxonomy_repo=TaxonomyRepo())
def exists_single(resource, sample_id):
return _exists(resource, sample_id, taxonomy_repo=TaxonomyRepo())
def resources():
taxonomy_repo = TaxonomyRepo()
ret_val = {
'resources': taxonomy_repo.resources(),
}
return jsonify(ret_val), 200
def setUp(self):
TempfileTestCase.setUp(self)
ConfigTestCase.setUp(self)
self.no_resources_repo = TaxonomyRepo()
self.table1_filename = self.create_tempfile(suffix='.qza').name
self.taxonomy1_filename = self.create_tempfile(suffix='.qza').name
self.table2_filename = self.create_tempfile(suffix='.qza').name
self.taxonomy2_filename = self.create_tempfile(suffix='.qza').name
self.table3_filename = self.create_tempfile(suffix='.qza').name
self.var_table_filename = self.create_tempfile(suffix='.qza').name
self.table_biom = self.create_tempfile(suffix='.biom').name
self.table = biom.Table(np.array([[0, 1, 2], [2, 4, 6], [3, 0, 1]]),
['feature-1', 'feature-2', 'feature-3'],
['sample-1', 'sample-2', 'sample-3'])
self.taxonomy_df = pd.DataFrame(
[['feature-1', 'a; b; c', 0.123],
['feature-2', 'a; b; c; d; e', 0.345],
['feature-3', 'a; f; g; h', 0.678]],
columns=['Feature ID', 'Taxon', 'Confidence'])
self.taxonomy_df.set_index('Feature ID', inplace=True)
self.table2 = biom.Table(np.array([[0, 1, 2], [2, 4, 6], [3, 0, 1]]),
['feature-1', 'feature-X', 'feature-3'],
['sample-1', 'sample-2', 'sample-3'])
self.taxonomy2_df = pd.DataFrame(
[['feature-1', 'a; b; c', 0.123],
['feature-X', 'a; b; c; d; e', 0.34],
['feature-3', 'a; f; g; h', 0.678]],
columns=['Feature ID', 'Taxon', 'Confidence'])
self.taxonomy2_df.set_index('Feature ID', inplace=True)
self.table3 = biom.Table(np.array([[1, 2], [0, 1]]),
['feature-X', 'feature-3'],
['sample-2', 'sample-3'])
imported_artifact = Artifact.import_data("FeatureTable[Frequency]",
self.table)
imported_artifact.save(self.table1_filename)
imported_artifact = Artifact.import_data("FeatureData[Taxonomy]",
self.taxonomy_df)
imported_artifact.save(self.taxonomy1_filename)
imported_artifact = Artifact.import_data("FeatureTable[Frequency]",
self.table2)
imported_artifact.save(self.table2_filename)
imported_artifact = Artifact.import_data("FeatureData[Taxonomy]",
self.taxonomy2_df)
imported_artifact.save(self.taxonomy2_filename)
imported_artifact = Artifact.import_data("FeatureTable[Frequency]",
self.table3)
imported_artifact.save(self.table3_filename)
with biom_open(self.table_biom, 'w') as f:
self.table.to_hdf5(f, 'test-table')
config.resources.update({
'table_resources': {
'table1': {
'table': self.table1_filename,
},
'table2': {
'table': self.table1_filename,
'feature-data-taxonomy': self.taxonomy1_filename,
'cache-taxonomy': False,
},
'table3': {
'table': self.table3_filename,
'feature-data-taxonomy': self.taxonomy2_filename,
'cache-taxonomy': False,
'variances': self.table3_filename,
},
'table4': {
'table': self.table_biom,
'feature-data-taxonomy': self.taxonomy1_filename,
'cache-taxonomy': False,
'table-format': 'biom'
},
'table5': {
'table': self.table2_filename,
},
'table6': {
'table': self.table_biom,
'table-format': 'biom',
},
'cached-taxonomy-table': {
'table': self.table1_filename,
'feature-data-taxonomy': self.taxonomy1_filename,
'cache-taxonomy': True,
},
}
})
resources.update(config.resources)
self.repo = TaxonomyRepo()
class TestTaxonomyRepoWithResources(TempfileTestCase, ConfigTestCase):
def setUp(self):
TempfileTestCase.setUp(self)
ConfigTestCase.setUp(self)
self.no_resources_repo = TaxonomyRepo()
self.table1_filename = self.create_tempfile(suffix='.qza').name
self.taxonomy1_filename = self.create_tempfile(suffix='.qza').name
self.table2_filename = self.create_tempfile(suffix='.qza').name
self.taxonomy2_filename = self.create_tempfile(suffix='.qza').name
self.table3_filename = self.create_tempfile(suffix='.qza').name
self.var_table_filename = self.create_tempfile(suffix='.qza').name
self.table_biom = self.create_tempfile(suffix='.biom').name
self.table = biom.Table(np.array([[0, 1, 2], [2, 4, 6], [3, 0, 1]]),
['feature-1', 'feature-2', 'feature-3'],
['sample-1', 'sample-2', 'sample-3'])
self.taxonomy_df = pd.DataFrame(
[['feature-1', 'a; b; c', 0.123],
['feature-2', 'a; b; c; d; e', 0.345],
['feature-3', 'a; f; g; h', 0.678]],
columns=['Feature ID', 'Taxon', 'Confidence'])
self.taxonomy_df.set_index('Feature ID', inplace=True)
self.table2 = biom.Table(np.array([[0, 1, 2], [2, 4, 6], [3, 0, 1]]),
['feature-1', 'feature-X', 'feature-3'],
['sample-1', 'sample-2', 'sample-3'])
self.taxonomy2_df = pd.DataFrame(
[['feature-1', 'a; b; c', 0.123],
['feature-X', 'a; b; c; d; e', 0.34],
['feature-3', 'a; f; g; h', 0.678]],
columns=['Feature ID', 'Taxon', 'Confidence'])
self.taxonomy2_df.set_index('Feature ID', inplace=True)
self.table3 = biom.Table(np.array([[1, 2], [0, 1]]),
['feature-X', 'feature-3'],
['sample-2', 'sample-3'])
imported_artifact = Artifact.import_data("FeatureTable[Frequency]",
self.table)
imported_artifact.save(self.table1_filename)
imported_artifact = Artifact.import_data("FeatureData[Taxonomy]",
self.taxonomy_df)
imported_artifact.save(self.taxonomy1_filename)
imported_artifact = Artifact.import_data("FeatureTable[Frequency]",
self.table2)
imported_artifact.save(self.table2_filename)
imported_artifact = Artifact.import_data("FeatureData[Taxonomy]",
self.taxonomy2_df)
imported_artifact.save(self.taxonomy2_filename)
imported_artifact = Artifact.import_data("FeatureTable[Frequency]",
self.table3)
imported_artifact.save(self.table3_filename)
with biom_open(self.table_biom, 'w') as f:
self.table.to_hdf5(f, 'test-table')
config.resources.update({
'table_resources': {
'table1': {
'table': self.table1_filename,
},
'table2': {
'table': self.table1_filename,
'feature-data-taxonomy': self.taxonomy1_filename,
'cache-taxonomy': False,
},
'table3': {
'table': self.table3_filename,
'feature-data-taxonomy': self.taxonomy2_filename,
'cache-taxonomy': False,
'variances': self.table3_filename,
},
'table4': {
'table': self.table_biom,
'feature-data-taxonomy': self.taxonomy1_filename,
'cache-taxonomy': False,
'table-format': 'biom'
},
'table5': {
'table': self.table2_filename,
},
'table6': {
'table': self.table_biom,
'table-format': 'biom',
},
'cached-taxonomy-table': {
'table': self.table1_filename,
'feature-data-taxonomy': self.taxonomy1_filename,
'cache-taxonomy': True,
},
}
})
resources.update(config.resources)
self.repo = TaxonomyRepo()
def tearDown(self):
TempfileTestCase.tearDown(self)
ConfigTestCase.tearDown(self)
def test_available_taxonomy_tables(self):
exp = ['table2', 'table3', 'table4', 'cached-taxonomy-table']
obs = self.repo.resources()
self.assertCountEqual(exp, obs)
def test_available_taxonomy_tables_empty_repo(self):
exp = []
obs = self.no_resources_repo.resources()
self.assertCountEqual(exp, obs)
def test_get_table(self):
exp = self.table
obs = self.repo.table('table2')
self.assertEqual(exp, obs)
def test_get_table_cached_taxonomy(self):
exp = self.table
obs = self.repo.table('cached-taxonomy-table')
self.assertEqual(exp, obs)
def test_get_table_invalid(self):
with self.assertRaises(ValueError):
self.repo.table('table1')
def test_get_taxonomy(self):
exp = self.taxonomy_df
obs = self.repo.feature_data_taxonomy('table4')
obs['Confidence'] = obs['Confidence'].astype('float64')
assert_frame_equal(exp, obs)
def test_get_taxonomy_model_cached(self):
exp = resources['table_resources']['cached-taxonomy-table']['model']
obs = self.repo.model('cached-taxonomy-table')
self.assertIs(exp, obs)
def test_get_taxonomy_model_non_cached(self):
self.assertNotIn('model', resources['table_resources']['table2'])
obs = self.repo.model('table2')
self.assertIsInstance(obs, TaxonomyModel)
def test_get_taxonomy_invalid(self):
with self.assertRaises(ValueError):
self.repo.table('foo')
def test_get_variances(self):
exp = self.table3
obs = self.repo.variances('table3')
self.assertEqual(exp, obs)
def test_get_variances_none(self):
exp = None
obs = self.repo.variances('table4')
self.assertIs(exp, obs)
def test_get_variances_invalid(self):
with self.assertRaises(ValueError):
self.repo.table('table6')
def test_exists(self):
exp = [False, True, True]
obs = self.repo.exists(['sample-1', 'sample-2', 'sample-3'], 'table3')
self.assertListEqual(exp, obs)
def test_exists_single(self):
obs = self.repo.exists('sample-1', 'table2')
self.assertTrue(obs)