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)
def test_heel_analyses(self):
# Long-running test
self._load_dataset()
# populate achilles first
test_util.get_synpuf_results_files()
test_util.populate_achilles(self.hpo_bucket, include_heel=False)
achilles_heel.create_tables(FAKE_HPO_ID, True)
achilles_heel.run_heel(hpo_id=FAKE_HPO_ID)
cmd = validation.sql_wrangle.qualify_tables(
'SELECT COUNT(1) FROM %sachilles_heel_results' % validation.sql_wrangle.PREFIX_PLACEHOLDER, FAKE_HPO_ID)
result = bq_utils.query(cmd)
self.assertEqual(int(result['rows'][0]['f'][0]['v']), ACHILLES_HEEL_RESULTS_COUNT)
cmd = validation.sql_wrangle.qualify_tables(
'SELECT COUNT(1) FROM %sachilles_results_derived' % validation.sql_wrangle.PREFIX_PLACEHOLDER, FAKE_HPO_ID)
result = bq_utils.query(cmd)
self.assertEqual(int(result['rows'][0]['f'][0]['v']), ACHILLES_RESULTS_DERIVED_COUNT)
def test_heel_analyses(self):
# Long-running test
self._load_dataset()
# populate achilles first
test_util.get_synpuf_results_files()
test_util.populate_achilles(self.hpo_bucket, include_heel=False)
achilles_heel.create_tables(FAKE_HPO_ID, True)
achilles_heel.run_heel(hpo_id=FAKE_HPO_ID)
cmd = validation.sql_wrangle.qualify_tables(
'SELECT COUNT(1) FROM %sachilles_heel_results' % validation.sql_wrangle.PREFIX_PLACEHOLDER, FAKE_HPO_ID)
result = bq_utils.query(cmd)
self.assertEqual(ACHILLES_HEEL_RESULTS_COUNT, int(result['rows'][0]['f'][0]['v']))
cmd = validation.sql_wrangle.qualify_tables(
'SELECT COUNT(1) FROM %sachilles_results_derived' % validation.sql_wrangle.PREFIX_PLACEHOLDER, FAKE_HPO_ID)
result = bq_utils.query(cmd)
self.assertEqual(ACHILLES_RESULTS_DERIVED_COUNT, int(result['rows'][0]['f'][0]['v']))
# test new heel re-categorization
errors = [2, 4, 5, 101, 200, 206, 207, 209, 400, 405, 406, 409, 411, 413, 500, 505, 506, 509,
600, 605, 606, 609, 613, 700, 705, 706, 709, 711, 713, 715, 716, 717, 800, 805, 806,
809, 813, 814, 906, 1006, 1609, 1805]
cmd = validation.sql_wrangle.qualify_tables(
"""SELECT analysis_id FROM {prefix}achilles_heel_results
WHERE achilles_heel_warning like 'ERROR:%'
GROUP BY analysis_id""".format(prefix=validation.sql_wrangle.PREFIX_PLACEHOLDER),
FAKE_HPO_ID)
result = bq_utils.query(cmd)
# self.assertIsNone(result.get('analysis_id', None))
actual_result = [int(row['f'][0]['v']) for row in result['rows']]
for analysis_id in actual_result:
self.assertIn(analysis_id, errors)
# self.assertEqual(ACHILLES_HEEL_RESULTS_ERROR_COUNT, int(result['rows'][0]['f'][0]['v']))
warnings = [4, 5, 7, 8, 9, 200, 210, 302, 400, 402, 412, 420,
500, 511, 512, 513, 514, 515,
602, 612, 620, 702, 712, 720, 802, 812, 820]
cmd = validation.sql_wrangle.qualify_tables(
"""SELECT analysis_id FROM {prefix}achilles_heel_results
WHERE achilles_heel_warning like 'WARNING:%'
GROUP BY analysis_id""".format(prefix=validation.sql_wrangle.PREFIX_PLACEHOLDER),
FAKE_HPO_ID)
result = bq_utils.query(cmd)
# self.assertIsNone(result.get('analysis_id', None))
actual_result = [int(row['f'][0]['v']) for row in result['rows']]
for analysis_id in actual_result:
self.assertIn(analysis_id, warnings)
# self.assertEqual(ACHILLES_HEEL_RESULTS_WARNING_COUNT, int(result['rows'][0]['f'][0]['v']))
notifications = [101, 103, 105, 114, 115, 118, 208, 301, 410, 610,
710, 810, 900, 907, 1000, 1800, 1807]
cmd = validation.sql_wrangle.qualify_tables(
"""SELECT analysis_id FROM {prefix}achilles_heel_results
WHERE achilles_heel_warning like 'NOTIFICATION:%' and analysis_id is not null
GROUP BY analysis_id""".format(prefix=validation.sql_wrangle.PREFIX_PLACEHOLDER),
FAKE_HPO_ID)
result = bq_utils.query(cmd)
self.assertIsNone(result.get('analysis_id', None))
actual_result = [int(row['f'][0]['v']) for row in result['rows']]
for analysis_id in actual_result:
self.assertIn(analysis_id, notifications)
def test_heel_analyses(self, mock_hpo_bucket):
# Long-running test
mock_hpo_bucket.return_value = self.get_mock_hpo_bucket()
# create randomized tables to bypass BQ rate limits
random_string = str(randint(10000, 99999))
randomized_hpo_id = FAKE_HPO_ID + '_' + random_string
# prepare
self._load_dataset(randomized_hpo_id)
test_util.populate_achilles(hpo_id=randomized_hpo_id,
include_heel=False)
# define tables
achilles_heel_results = randomized_hpo_id + '_' + achilles_heel.ACHILLES_HEEL_RESULTS
achilles_results_derived = randomized_hpo_id + '_' + achilles_heel.ACHILLES_RESULTS_DERIVED
# run achilles heel
achilles_heel.create_tables(randomized_hpo_id, True)
achilles_heel.run_heel(hpo_id=randomized_hpo_id)
# validate
query = sql_wrangle.qualify_tables(
'SELECT COUNT(1) as num_rows FROM %s' % achilles_heel_results)
response = bq_utils.query(query)
rows = bq_utils.response2rows(response)
self.assertEqual(ACHILLES_HEEL_RESULTS_COUNT, rows[0]['num_rows'])
query = sql_wrangle.qualify_tables(
'SELECT COUNT(1) as num_rows FROM %s' % achilles_results_derived)
response = bq_utils.query(query)
rows = bq_utils.response2rows(response)
self.assertEqual(ACHILLES_RESULTS_DERIVED_COUNT, rows[0]['num_rows'])
# test new heel re-categorization
errors = [
2, 4, 5, 101, 200, 206, 207, 209, 400, 405, 406, 409, 411, 413,
500, 505, 506, 509, 600, 605, 606, 609, 613, 700, 705, 706, 709,
711, 713, 715, 716, 717, 800, 805, 806, 809, 813, 814, 906, 1006,
1609, 1805
]
query = sql_wrangle.qualify_tables(
"""SELECT analysis_id FROM {table_id}
WHERE achilles_heel_warning LIKE 'ERROR:%'
GROUP BY analysis_id""".format(table_id=achilles_heel_results))
response = bq_utils.query(query)
rows = bq_utils.response2rows(response)
actual_result = [row["analysis_id"] for row in rows]
for analysis_id in actual_result:
self.assertIn(analysis_id, errors)
warnings = [
4, 5, 7, 8, 9, 200, 210, 302, 400, 402, 412, 420, 500, 511, 512,
513, 514, 515, 602, 612, 620, 702, 712, 720, 802, 812, 820
]
query = sql_wrangle.qualify_tables(
"""SELECT analysis_id FROM {table_id}
WHERE achilles_heel_warning LIKE 'WARNING:%'
GROUP BY analysis_id""".format(table_id=achilles_heel_results))
response = bq_utils.query(query)
rows = bq_utils.response2rows(response)
actual_result = [row["analysis_id"] for row in rows]
for analysis_id in actual_result:
self.assertIn(analysis_id, warnings)
notifications = [
101, 103, 105, 114, 115, 118, 208, 301, 410, 610, 710, 810, 900,
907, 1000, 1800, 1807
]
query = sql_wrangle.qualify_tables(
"""SELECT analysis_id FROM {table_id}
WHERE achilles_heel_warning LIKE 'NOTIFICATION:%' and analysis_id is not null
GROUP BY analysis_id""".format(table_id=achilles_heel_results))
response = bq_utils.query(query)
rows = bq_utils.response2rows(response)
actual_result = [row["analysis_id"] for row in rows]
for analysis_id in actual_result:
self.assertIn(analysis_id, notifications)