def test_load_analyses(self):
achilles.create_tables(FAKE_HPO_ID, True)
achilles.load_analyses(FAKE_HPO_ID)
cmd = validation.sql_wrangle.qualify_tables(
'SELECT DISTINCT(analysis_id) FROM %sachilles_analysis' % validation.sql_wrangle.PREFIX_PLACEHOLDER, FAKE_HPO_ID)
result = bq_utils.query(cmd)
self.assertEqual(ACHILLES_LOOKUP_COUNT, int(result['totalRows']))
def test_run_analyses(self):
# Long-running test
self._load_dataset()
achilles.create_tables(FAKE_HPO_ID, True)
achilles.load_analyses(FAKE_HPO_ID)
achilles.run_analyses(hpo_id=FAKE_HPO_ID)
cmd = validation.sql_wrangle.qualify_tables(
'SELECT COUNT(1) FROM %sachilles_results' % validation.sql_wrangle.PREFIX_PLACEHOLDER, FAKE_HPO_ID)
result = bq_utils.query(cmd)
self.assertEqual(int(result['rows'][0]['f'][0]['v']), ACHILLES_RESULTS_COUNT)
def run_achilles(hpo_id=None):
"""checks for full results and run achilles/heel
:hpo_id: hpo on which to run achilles
:returns:
"""
if hpo_id is not None:
logging.info('running achilles for hpo_id %s' % hpo_id)
achilles.create_tables(hpo_id, True)
achilles.load_analyses(hpo_id)
achilles.run_analyses(hpo_id=hpo_id)
if hpo_id is not None:
logging.info('running achilles_heel for hpo_id %s' % hpo_id)
achilles_heel.create_tables(hpo_id, True)
achilles_heel.run_heel(hpo_id=hpo_id)
