def setUp(self):
ConfigTestCase.setUp(self)
TempfileTestCase.setUp(self)
self.no_resources_repo = AlphaRepo()
resource_filename1 = self.create_tempfile(suffix='.qza').name
resource_filename2 = self.create_tempfile(suffix='.qza').name
test_series1 = pd.Series({
'sample1': 7.15,
'sample2': 9.04
},
name='chao1')
test_series2 = pd.Series(
{
'sample3': 7.24,
'sample2': 9.04,
'sample4': 8.25
},
name='faith_pd')
imported_artifact = Artifact.import_data("SampleData[AlphaDiversity]",
test_series1)
imported_artifact.save(resource_filename1)
imported_artifact = Artifact.import_data("SampleData[AlphaDiversity]",
test_series2)
imported_artifact.save(resource_filename2)
config.resources.update({
'alpha_resources': {
'chao1': resource_filename1,
'faith_pd': resource_filename2,
}
})
resources.update(config.resources)
self.repo = AlphaRepo()
def available_metrics_alpha():
alpha_repo = AlphaRepo()
ret_val = {
'alpha_metrics': alpha_repo.available_metrics(),
}
return jsonify(ret_val), 200
def test_load_resource_metric_not_available(self):
alpha_repo = AlphaRepo()
with patch.object(AlphaRepo, 'available_metrics') as mock_avail:
mock_avail.return_value = ['faith_pd', 'chao1']
with self.assertRaisesRegex(
UnknownMetric, "No resource "
"available for "
"metric="
"'fake-test-metric'"):
alpha_repo._get_resource('fake-test-metric')
def alpha_group(body,
alpha_metric,
summary_statistics=True,
percentiles=None,
return_raw=False):
if not (summary_statistics or return_raw):
# swagger does not account for parameter dependencies, so we should
# give a bad request error here
return jsonify(error=400,
text='Either `summary_statistics`, `return_raw`, '
'or both are required to be true.'), 400
sample_ids = body['sample_ids']
alpha_repo = AlphaRepo()
# figure out if the user asked for a metric we have data on
available_metrics = alpha_repo.available_metrics()
type_ = 'metric'
missing_metric = validate_resource(available_metrics, alpha_metric, type_)
if missing_metric:
return missing_metric
# make sure all of the data the samples the user asked for have values
# for the given metric
missing_ids = [
id_ for id_ in sample_ids if not alpha_repo.exists(id_, alpha_metric)
]
missing_ids_msg = check_missing_ids(missing_ids, alpha_metric, type_)
if missing_ids_msg:
return missing_ids_msg
# retrieve the alpha diversity for each sample
alpha_series = alpha_repo.get_alpha_diversity(
sample_ids,
alpha_metric,
)
alpha_ = Alpha(alpha_series, percentiles=percentiles)
alpha_data = dict()
if return_raw:
# not using name right now, so give it a placeholder name
alpha_values = alpha_.get_group_raw(name='').to_dict()
del alpha_values['name']
alpha_data.update(alpha_values)
if summary_statistics:
# not using name right now, so give it a placeholder name
alpha_summary = alpha_.get_group(name='').to_dict()
del alpha_summary['name']
alpha_data.update({'alpha_metric': alpha_summary.pop('alpha_metric')})
alpha_data.update({'group_summary': alpha_summary})
response = jsonify(alpha_data)
return response, 200
def _get_alpha_info(alpha_metric, matching_ids, percentiles, sample_id):
alpha_repo = AlphaRepo()
# retrieve the alpha diversity for each sample
alpha_series = alpha_repo.get_alpha_diversity(
matching_ids,
alpha_metric,
)
alpha_ = Alpha(alpha_series, percentiles=percentiles)
alpha_summary = alpha_.get_group(name='').to_dict()
if sample_id:
sample_diversity, = alpha_repo.get_alpha_diversity(
sample_id, alpha_metric)
else:
sample_diversity = None
return alpha_summary, sample_diversity
def get_alpha(sample_id, alpha_metric):
alpha_repo = AlphaRepo()
if not all(alpha_repo.exists([sample_id], alpha_metric)):
return jsonify(error=404, text="Sample ID not found."), \
404
alpha_series = alpha_repo.get_alpha_diversity([sample_id], alpha_metric)
alpha_ = Alpha(alpha_series)
alpha_data = alpha_.get_group_raw().to_dict()
ret_val = {
'sample_id': sample_id,
'alpha_metric': alpha_data['alpha_metric'],
'data': alpha_data['alpha_diversity'][sample_id],
}
return jsonify(ret_val), 200
def setUp(self):
super().setUp()
faith_pd_values = [1, 2, 3, 4]
faith_pd_index = ['s01', 's02', 's04', 's05']
shannon_values = [7.24, 9.05, 8.25]
shannon_index = ['s01', 's02', 'sOther']
alpha_resources = AlphaRepo({
'faith_pd':
pd.Series(faith_pd_values, index=faith_pd_index),
'shannon':
pd.Series(shannon_values, index=shannon_index),
})
self.res_patcher = patch(
'microsetta_public_api.api.plotting._alpha_repo_getter')
self.mock_resources = self.res_patcher.start()
self.mock_resources.return_value = alpha_resources
self.metadata = MetadataRepo(
pd.DataFrame(
{
'age_cat': ['30s', '40s', '50s', '30s', '30s'],
'num_var': [3, 4, 5, 6, 7],
},
index=['s01', 's02', 's04', 's05', 'sOther']))
self.md_patcher = patch(
'microsetta_public_api.api.plotting._metadata_repo_getter')
self.mock_metadata = self.md_patcher.start()
self.mock_metadata.return_value = self.metadata
def get_alpha_alt(dataset, sample_id, alpha_metric):
alpha_resource = _validate_dataset_alpha(dataset, get_resources)
alpha_repo = AlphaRepo(alpha_resource.data)
alpha_value = _get_alpha(alpha_repo, alpha_metric, sample_id)
return jsonify(alpha_value), 200
def alpha_group(body,
alpha_metric,
summary_statistics=True,
percentiles=None,
return_raw=False):
alpha_repo = AlphaRepo()
alpha_data = _alpha_group(body, alpha_repo, _metadata_repo_getter,
alpha_metric, percentiles, return_raw,
summary_statistics)
response = jsonify(alpha_data)
return response, 200
def alpha_group_alt(body,
dataset,
alpha_metric,
summary_statistics=True,
percentiles=None,
return_raw=False):
alpha_resource = _validate_dataset_alpha(dataset, get_resources)
alpha_repo = AlphaRepo(alpha_resource.data)
getter = partial(_metadata_repo_getter_alt, dataset=dataset)
alpha_data = _alpha_group(body, alpha_repo, getter, alpha_metric,
percentiles, return_raw, summary_statistics)
return jsonify(alpha_data), 200
def _alpha_repo_getter():
return AlphaRepo()
def available_metrics_alpha():
alpha_repo = AlphaRepo()
ret_val = _available_metrics(alpha_repo)
return jsonify(ret_val), 200
def available_metrics_alpha_alt(dataset):
alpha_resource = _validate_dataset_alpha(dataset, get_resources)
alpha_repo = AlphaRepo(alpha_resource.data)
return jsonify(_available_metrics(alpha_repo)), 200
class TestAlphaRepoWithResources(TempfileTestCase, ConfigTestCase):
def setUp(self):
ConfigTestCase.setUp(self)
TempfileTestCase.setUp(self)
self.no_resources_repo = AlphaRepo()
resource_filename1 = self.create_tempfile(suffix='.qza').name
resource_filename2 = self.create_tempfile(suffix='.qza').name
test_series1 = pd.Series({
'sample1': 7.15,
'sample2': 9.04
},
name='chao1')
test_series2 = pd.Series(
{
'sample3': 7.24,
'sample2': 9.04,
'sample4': 8.25
},
name='faith_pd')
imported_artifact = Artifact.import_data("SampleData[AlphaDiversity]",
test_series1)
imported_artifact.save(resource_filename1)
imported_artifact = Artifact.import_data("SampleData[AlphaDiversity]",
test_series2)
imported_artifact.save(resource_filename2)
config.resources.update({
'alpha_resources': {
'chao1': resource_filename1,
'faith_pd': resource_filename2,
}
})
resources.update(config.resources)
self.repo = AlphaRepo()
def tearDown(self):
TempfileTestCase.tearDown(self)
ConfigTestCase.tearDown(self)
def test_available_metrics(self):
exp = ['chao1', 'faith_pd']
obs = self.repo.available_metrics()
self.assertCountEqual(exp, obs)
def test_get_alpha_diversity(self):
# group tests
obs = self.repo.get_alpha_diversity(['sample2', 'sample1'], 'chao1')
exp_series = pd.Series([9.04, 7.15],
index=['sample2', 'sample1'],
name='chao1')
assert_series_equal(obs, exp_series)
def test_get_alpha_diversity_single_sample(self):
# single sample tests
obs = self.repo.get_alpha_diversity('sample2', 'chao1')
exp_series = pd.Series([9.04], index=['sample2'], name='chao1')
assert_series_equal(obs, exp_series)
def test_exists(self):
# group tests
sample_list = ['sample2', 'sample1', 'sample2', 'blah', 'sample4']
obs = self.repo.exists(sample_list, 'chao1')
exp = [True, True, True, False, False]
self.assertListEqual(obs, exp)
obs = self.repo.exists(sample_list, 'faith_pd')
exp = [True, False, True, False, True]
self.assertListEqual(obs, exp)
def test_exists_single_sample(self):
# single sample tests
obs = self.repo.exists('sample1', 'chao1')
self.assertTrue(obs)
obs = self.repo.exists('sample1', 'faith_pd')
self.assertFalse(obs)
def exists_single_alt(dataset, alpha_metric, sample_id):
alpha_resource = _validate_dataset_alpha(dataset, get_resources)
alpha_repo = AlphaRepo(alpha_resource.data)
return _exists(alpha_repo, alpha_metric, sample_id)
def exists_single(alpha_metric, sample_id):
alpha_repo = AlphaRepo()
return _exists(alpha_repo, alpha_metric, sample_id)
def exists_group_alt(body, dataset, alpha_metric):
alpha_resource = _validate_dataset_alpha(dataset, get_resources)
alpha_repo = AlphaRepo(alpha_resource.data)
return _exists(alpha_repo, alpha_metric, body)
def exists_group(body, alpha_metric):
alpha_repo = AlphaRepo()
return _exists(alpha_repo, alpha_metric, body)
def get_alpha(sample_id, alpha_metric):
alpha_repo = AlphaRepo()
ret_val = _get_alpha(alpha_repo, alpha_metric, sample_id)
return jsonify(ret_val), 200
def _getter():
alpha_resource = _validate_dataset_alpha(dataset, get_resources)
return AlphaRepo(alpha_resource.data)