def run_analyses(hpo_id):
"""
Run the achilles analyses
:param hpo_id:
:return:
"""
commands = _get_run_analysis_commands(hpo_id)
for command in commands:
logging.debug(' ---- Running `%s`...\n' % command)
if sql_wrangle.is_to_temp_table(command):
table_id = sql_wrangle.get_temp_table_name(command)
query = sql_wrangle.get_temp_table_query(command)
insert_query_job_result = bq_utils.query(query, False, table_id)
query_job_id = insert_query_job_result['jobReference']['jobId']
incomplete_jobs = bq_utils.wait_on_jobs([query_job_id])
if len(incomplete_jobs) > 0:
logging.critical('tempresults doesnt get created in 15 secs')
raise RuntimeError('Tempresults taking too long to create')
elif sql_wrangle.is_truncate(command):
table_id = sql_wrangle.get_truncate_table_name(command)
if bq_utils.table_exists(table_id):
bq_utils.delete_table(table_id)
elif sql_wrangle.is_drop(command):
table_id = sql_wrangle.get_drop_table_name(command)
if bq_utils.table_exists(table_id):
bq_utils.delete_table(table_id)
else:
bq_utils.query(command)
def run_heel(hpo_id):
"""
Run heel commands
:param hpo_id: string name for the hpo identifier
:returns: None
:raises RuntimeError: Raised if BigQuery takes longer than 30 seconds
to complete a job on a temporary table
"""
# very long test
commands = _get_heel_commands(hpo_id)
count = 0
for command in commands:
count = count + 1
logging.debug(' ---- running query # {}'.format(count))
logging.debug(' ---- Running `%s`...\n' % command)
if sql_wrangle.is_to_temp_table(command):
table_id = sql_wrangle.get_temp_table_name(command)
query = sql_wrangle.get_temp_table_query(command)
insert_query_job_result = bq_utils.query(query, False, table_id)
query_job_id = insert_query_job_result['jobReference']['jobId']
incomplete_jobs = bq_utils.wait_on_jobs([query_job_id])
if len(incomplete_jobs) > 0:
logging.critical('tempresults doesnt get created in 30 secs')
raise RuntimeError('Tempresults taking too long to create')
elif sql_wrangle.is_truncate(command):
table_id = sql_wrangle.get_truncate_table_name(command)
query = 'DELETE FROM %s WHERE TRUE' % table_id
bq_utils.query(query)
elif sql_wrangle.is_drop(command):
table_id = sql_wrangle.get_drop_table_name(command)
bq_utils.delete_table(table_id)
else:
bq_utils.query(command)
def run_heel(hpo_id):
# very long test
commands = _get_heel_commands(hpo_id)
count = 0
for command in commands:
count = count + 1
logging.debug(' ---- running query # {}'.format(count))
logging.debug(' ---- Running `%s`...\n' % command)
if sql_wrangle.is_to_temp_table(command):
table_id = sql_wrangle.get_temp_table_name(command)
query = sql_wrangle.get_temp_table_query(command)
insert_query_job_result = bq_utils.query(query, False, table_id)
query_job_id = insert_query_job_result['jobReference']['jobId']
incomplete_jobs = bq_utils.wait_on_jobs([query_job_id])
if len(incomplete_jobs) > 0:
logging.critical('tempresults doesnt get created in 30 secs')
raise RuntimeError('Tempresults taking too long to create')
elif sql_wrangle.is_truncate(command):
table_id = sql_wrangle.get_truncate_table_name(command)
query = 'DELETE FROM %s WHERE TRUE' % table_id
bq_utils.query(query)
elif sql_wrangle.is_drop(command):
table_id = sql_wrangle.get_drop_table_name(command)
bq_utils.delete_table(table_id)
else:
bq_utils.query(command)
time.sleep(1)