def test_finalizer_update(
self, mock_feature_transformer, mock_fetch_annotations,
mock_analysis_transformer, mock_specimen_library_transformer,
mock_project_publication_contributor_transformer, mock_log_error,
mock_upload_and_load, mock_swagger_spec):
mock_swagger_spec.return_value = self.stub_swagger_spec
extractor = DSSExtractor(staging_directory="test_dir",
content_type_patterns=[],
filename_patterns=[],
dss_client=get_dss_client("dev"))
finalizer_update(extractor)
mock_feature_transformer.assert_called_once_with("test_dir/bundles")
mock_analysis_transformer.assert_called_once_with("test_dir/bundles")
mock_specimen_library_transformer.assert_called_once_with(
"test_dir/bundles")
mock_project_publication_contributor_transformer.assert_called_once_with(
"test_dir/bundles")
mock_upload_and_load.assert_called_once_with("test_dir",
is_update=True)
e = Exception()
mock_upload_and_load.reset_mock()
mock_analysis_transformer.side_effect = e
finalizer_update(extractor)
mock_log_error.assert_called_once_with("AnalysisTransformer", e,
mock.ANY, extractor)
mock_upload_and_load.assert_called_once_with("test_dir",
is_update=True)
def read_bundle(fqid):
dss_client = get_dss_client(os.environ['DEPLOYMENT_STAGE'])
bundle_uuid, bundle_version = fqid.split(".", 1)
bundle = dss_client.get_bundle(uuid=bundle_uuid,
version=bundle_version,
replica="aws")
rsem_file = [
f for f in bundle['bundle']['files']
if f["name"].endswith(".genes.results")
][0]
rsem_contents = dss_client.get_file(uuid=rsem_file["uuid"],
version=rsem_file["version"],
replica="aws")
rsem_reader = csv.DictReader(io.StringIO(rsem_contents.decode()),
delimiter="\t")
bundle_expression_sum = 0
bundle_expression_nonzeros = set()
for row in rsem_reader:
bundle_expression_sum += float(row["expected_count"])
if float(row['expected_count']) != 0.0:
bundle_expression_nonzeros.add(row["gene_id"].split(".", 1)[0])
return {
"expression_sum": bundle_expression_sum,
"expression_nonzero": len(bundle_expression_nonzeros),
"cell_count": 1
}
def test_get_dss_client(self, mock_swagger_spec):
mock_swagger_spec.return_value = self.stub_swagger_spec
self.stub_swagger_spec[
'host'] = "dss.integration.data.humancellatlas.org"
self.assertEqual(
get_dss_client("integration").host,
"https://dss.integration.data.humancellatlas.org/v1")
self.stub_swagger_spec['host'] = "dss.staging.data.humancellatlas.org"
self.assertEqual(
get_dss_client("staging").host,
"https://dss.staging.data.humancellatlas.org/v1")
self.stub_swagger_spec['host'] = "dss.data.humancellatlas.org"
self.assertEqual(
get_dss_client("predev").host,
"https://dss.data.humancellatlas.org/v1")
self.assertEqual(
get_dss_client("dev").host,
"https://dss.data.humancellatlas.org/v1")
self.assertEqual(
get_dss_client("prod").host,
"https://dss.data.humancellatlas.org/v1")
def _verify_load(es_query):
dss_client = etl.get_dss_client(deployment_stage=os.environ['DEPLOYMENT_STAGE'])
response = dss_client.post_search.iterate(es_query=es_query,
replica='aws',
per_page=500)
expected_bundles = list(result['bundle_fqid'] for result in response)
print(f"Loading {len(expected_bundles)} bundles to {os.environ['DEPLOYMENT_STAGE']} complete.\n"
f"Verifying row counts in Redshift...")
redshift = RedshiftHandler()
count_bundles_query = f"SELECT COUNT(*) FROM analysis WHERE bundle_fqid IN {format_str_list(expected_bundles)}"
results = redshift.transaction(queries=[count_bundles_query],
return_results=True)
print(f"Found {results[0][0]} analysis rows for {len(expected_bundles)} expected bundles.")
assert (results[0][0] == len(expected_bundles))
def test_transform_bundle(self, mock_cell_expression_transform,
mock_log_error, mock_swagger_spec):
mock_swagger_spec.return_value = self.stub_swagger_spec
extractor = DSSExtractor(staging_directory="test_dir",
content_type_patterns=[],
filename_patterns=[],
dss_client=get_dss_client("dev"))
transform_bundle("test_uuid", "test_version", "test_path",
"test_manifest_path", extractor)
mock_cell_expression_transform.assert_called_once_with("test_path")
e = Exception()
mock_cell_expression_transform.side_effect = e
transform_bundle("test_uuid", "test_version", "test_path",
"test_manifest_path", extractor)
mock_log_error.assert_called_once_with("test_uuid.test_version", e,
mock.ANY, extractor)
def test_log_error(self, mock_error, mock_datetime_now, mock_swagger_spec):
mock_swagger_spec.return_value = self.stub_swagger_spec
mock_datetime_now.return_value = "timestamp"
ex = Exception("msg")
extractor = DSSExtractor(staging_directory="test_dir",
content_type_patterns=[],
filename_patterns=[],
dss_client=get_dss_client("dev"))
with mock.patch("builtins.open", mock.mock_open()) as mock_open:
_log_error("test_bundle", ex, "test_trace", extractor)
handle = mock_open()
expected_calls = [
mock.call(
"[timestamp] test_bundle failed with exception: msg\ntest_trace\n"
),
mock.call("test_bundle\n")
]
handle.write.assert_has_calls(expected_calls)
self.assertTrue(mock_error.called)
import json
import mock
import os
import boto3
from matrix.common import constants
from matrix.common.etl import get_dss_client
from scripts.dss_subscription import (recreate_dss_subscription,
_generate_metadata_schema_version_clause,
_regenerate_and_set_hmac_secret_key,
DSS_SUBSCRIPTION_HMAC_SECRET_ID)
from tests.unit import MatrixTestCaseUsingMockAWS
DSS_CLIENT = get_dss_client("dev")
class TestDssSubscription(MatrixTestCaseUsingMockAWS):
def setUp(self):
super(TestDssSubscription, self).setUp()
self.swagger_spec_stub = {
'info': {
'description': "test_description"
},
'host': "test_host",
'basePath': "/v1",
'paths': {}
}
@mock.patch("secrets.token_hex")
def test_regenerate_and_set_hmac_secret(self, mock_token_hex):
