def _present_microbes_taxonomy_table(sample_ids, resource):
taxonomy_repo = TaxonomyRepo()
error_response = _check_resource_and_missing_ids(taxonomy_repo, sample_ids,
resource)
if error_response:
return error_response
taxonomy_ = taxonomy_repo.model(resource)
taxonomy_table = taxonomy_.presence_data_table(sample_ids)
response = jsonify(taxonomy_table.to_dict())
return response, 200
def _summarize_group(sample_ids, table_name):
taxonomy_repo = TaxonomyRepo()
error_response = _check_resource_and_missing_ids(taxonomy_repo, sample_ids,
table_name)
if error_response:
return error_response
taxonomy_ = taxonomy_repo.model(table_name)
taxonomy_data = taxonomy_.get_group(sample_ids, '').to_dict()
del taxonomy_data['name']
del taxonomy_data['feature_ranks']
response = jsonify(taxonomy_data)
return response, 200
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)