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)