def _format_and_store_queries_in_s3(self, resolved_bundle_uuids: list,
genus_species: str):
feature_query = feature_query_template.format(
self.query_results_bucket, self.request_id, self.redshift_role_arn,
genus_species)
feature_query_obj_key = self.s3_handler.store_content_in_s3(
f"{self.request_id}/feature", feature_query)
exp_query = expression_query_template.format(
self.query_results_bucket, self.request_id, self.redshift_role_arn,
format_str_list(resolved_bundle_uuids), genus_species)
exp_query_obj_key = self.s3_handler.store_content_in_s3(
f"{self.request_id}/expression", exp_query)
cell_query = cell_query_template.format(
self.query_results_bucket, self.request_id, self.redshift_role_arn,
format_str_list(resolved_bundle_uuids), genus_species)
cell_query_obj_key = self.s3_handler.store_content_in_s3(
f"{self.request_id}/cell", cell_query)
return {
QueryType.CELL: cell_query_obj_key,
QueryType.EXPRESSION: exp_query_obj_key,
QueryType.FEATURE: feature_query_obj_key
}
def test_dss_notification(self):
bundle_data = NOTIFICATION_TEST_DATA[self.dss_env]
bundle_fqid = bundle_data['bundle_fqid']
cell_row_count = bundle_data['cell_count']
expression_row_count = bundle_data['exp_count']
cellkeys = format_str_list(self._get_cellkeys_from_fqid(bundle_fqid))
self.assertTrue(len(cellkeys) > 0)
try:
self._post_notification(bundle_fqid=bundle_fqid,
event_type="DELETE")
WaitFor(self._poll_db_get_row_counts_for_fqid, bundle_fqid, cellkeys)\
.to_return_value((0, 0, 0), timeout_seconds=60)
self._post_notification(bundle_fqid=bundle_fqid,
event_type="CREATE")
WaitFor(self._poll_db_get_row_counts_for_fqid, bundle_fqid, cellkeys)\
.to_return_value((1, cell_row_count, expression_row_count), timeout_seconds=600)
self._post_notification(bundle_fqid=bundle_fqid,
event_type="TOMBSTONE")
WaitFor(self._poll_db_get_row_counts_for_fqid, bundle_fqid, cellkeys)\
.to_return_value((0, 0, 0), timeout_seconds=60)
self._post_notification(bundle_fqid=bundle_fqid,
event_type="UPDATE")
WaitFor(self._poll_db_get_row_counts_for_fqid, bundle_fqid, cellkeys)\
.to_return_value((1, cell_row_count, expression_row_count), timeout_seconds=600)
finally:
self._post_notification(bundle_fqid=bundle_fqid,
event_type="CREATE")
def test_single_value(self):
values = ["id1.version"]
formatted_values = "('id1.version')"
self.assertEqual(query_constructor.format_str_list(values),
formatted_values)
def _format_and_store_queries_in_s3(self, resolved_bundle_fqids: list):
feature_query = feature_query_template.format(
self.query_results_bucket, self.request_id, self.redshift_role_arn)
feature_query_obj_key = self.s3_handler.store_content_in_s3(
f"{self.request_id}/feature", feature_query)
exp_query = expression_query_template.format(
self.query_results_bucket, self.request_id, self.redshift_role_arn,
format_str_list(resolved_bundle_fqids))
exp_query_obj_key = self.s3_handler.store_content_in_s3(
f"{self.request_id}/expression", exp_query)
cell_query = cell_query_template.format(
self.query_results_bucket, self.request_id, self.redshift_role_arn,
format_str_list(resolved_bundle_fqids))
cell_query_obj_key = self.s3_handler.store_content_in_s3(
f"{self.request_id}/cell", cell_query)
return [feature_query_obj_key, exp_query_obj_key, cell_query_obj_key]
def _fetch_bundle_count_from_analysis_table(self,
resolved_bundle_fqids: list):
analysis_table_bundle_count_query = analysis_bundle_count_query_template.format(
format_str_list(resolved_bundle_fqids))
analysis_table_bundle_count_query = analysis_table_bundle_count_query.strip(
).replace('\n', '')
results = self.redshift_handler.transaction(
[analysis_table_bundle_count_query],
read_only=True,
return_results=True)
analysis_table_bundle_count = results[0][0]
return analysis_table_bundle_count
