def test_timeout(self, mock_creation_date, mock_log_error):
# no timeout
mock_creation_date.return_value = date.to_string(
date.get_datetime_now() - timedelta(hours=35, minutes=59))
self.assertFalse(self.request_tracker.timeout)
# timeout
mock_creation_date.return_value = date.to_string(
date.get_datetime_now() - timedelta(hours=36, minutes=1))
self.assertTrue(self.request_tracker.timeout)
mock_log_error.assert_called_once()
def _test_converter_with_file_format(self,
file_format,
mock_s3_fs,
mock_s3_map,
mock_to_mtx,
mock_to_loom,
mock_to_csv,
mock_zipfile_write,
mock_mmwrite,
mock_s3_put,
mock_complete_subtask_execution,
mock_complete_request,
mock_parse_manifest,
mock_hstack,
mock_creation_date,
mock_os_mkdir,
mock_os_remove):
mock_s3_fs.return_value = None
mock_s3_map.return_value = None
mock_creation_date.return_value = date.to_string(datetime.datetime.utcnow())
main(["test_id", "test_exp_manifest", "test_cell_manifest",
"test_gene_manifest", "test_target", file_format, "."])
if file_format == "loom":
mock_to_loom.assert_called_once()
elif file_format == "csv":
mock_to_csv.assert_called_once()
elif file_format == "mtx":
mock_to_mtx.assert_called_once()
mock_s3_put.assert_called_once()
mock_complete_subtask_execution.assert_called_once_with(Subtask.CONVERTER)
mock_complete_request.assert_called_once_with(duration=mock.ANY)
def test_empty_results(self, mock_parse_manifest,
mock_upload_converted_matrix,
mock_complete_subtask_execution,
mock_complete_request, mock_creation_date,
mock_remove):
mock_creation_date.return_value = date.to_string(
datetime.datetime.utcnow())
self.matrix_converter.query_results = {
QueryType.CELL: CellQueryResultsReader("test_manifest_key"),
QueryType.EXPRESSION:
ExpressionQueryResultsReader("test_manifest_key"),
QueryType.FEATURE: FeatureQueryResultsReader("test_manifest_key")
}
mock_parse_manifest.return_value = {"record_count": 0}
self.matrix_converter.local_output_filename = "unit_test_empty_loom.loom"
self.matrix_converter.run()
self.assertEqual(os.path.getsize("unit_test_empty_loom.loom"), 0)
mock_complete_subtask_execution.assert_called_once_with(
Subtask.CONVERTER)
mock_complete_request.assert_called_once()
os.remove("unit_test_empty_loom.loom")
def test_is_expired(self, mock_exists, mock_creation_date, mock_log_error):
with self.subTest("Expired"):
mock_exists.return_value = False
mock_creation_date.return_value = date.to_string(
date.get_datetime_now() - timedelta(days=30, minutes=1))
self.assertTrue(self.request_tracker.is_expired)
mock_log_error.assert_called_once()
mock_log_error.reset_mock()
with self.subTest(
"Not expired. Matrix DNE but not past expiration date"):
mock_exists.return_value = False
mock_creation_date.return_value = date.to_string(
date.get_datetime_now() - timedelta(days=29))
self.assertFalse(self.request_tracker.is_expired)
mock_log_error.assert_not_called()
with self.subTest("Not expired. Matrix exists"):
mock_exists.return_value = True
self.assertFalse(self.request_tracker.is_expired)
mock_log_error.assert_not_called()
def test_run(self, mock_parse_manifest, mock_to_loom,
mock_upload_converted_matrix, mock_subtask_exec,
mock_complete_request, mock_creation_date, mock_os_remove):
mock_creation_date.return_value = date.to_string(
datetime.datetime.utcnow())
mock_to_loom.return_value = "local_matrix_path"
self.matrix_converter.run()
mock_manifest_calls = [
mock.call("test_exp_manifest"),
mock.call("test_cell_manifest"),
mock.call("test_gene_manifest")
]
mock_parse_manifest.assert_has_calls(mock_manifest_calls)
mock_to_loom.assert_called_once()
mock_subtask_exec.assert_called_once_with(Subtask.CONVERTER)
mock_complete_request.assert_called_once
mock_upload_converted_matrix.assert_called_once_with(
"local_matrix_path", "test_target")
def test_conversions(self):
self.assertEqual(date.to_datetime(date.to_string(self.now)), self.now)