def test_ehr_person_to_observation_counts(self):
self._load_datasets()
# perform ehr union
ehr_union.main(self.input_dataset_id, self.output_dataset_id,
self.project_id, self.hpo_ids)
q_person = '''
SELECT *
FROM {output_dataset_id}.unioned_ehr_person AS p
'''.format(output_dataset_id=self.output_dataset_id)
person_response = bq_utils.query(q_person)
person_rows = bq_utils.response2rows(person_response)
q_observation = '''
SELECT *
FROM {output_dataset_id}.unioned_ehr_observation
WHERE observation_type_concept_id = 38000280
'''.format(output_dataset_id=self.output_dataset_id)
# observation should contain 4 records per person of type EHR
expected = len(person_rows) * 4
observation_response = bq_utils.query(q_observation)
observation_rows = bq_utils.response2rows(observation_response)
actual = len(observation_rows)
self.assertEqual(
actual, expected,
'Expected %s EHR person records in observation but found %s' %
(expected, actual))
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 test_ehr_person_to_observation_counts(self, mock_tables_map):
self._load_datasets()
mock_tables_map.return_value = [
common.OBSERVATION, common.LOCATION, common.CARE_SITE,
common.VISIT_OCCURRENCE
]
# perform ehr union
ehr_union.main(self.input_dataset_id, self.output_dataset_id,
self.project_id, self.hpo_ids)
q_person = '''
SELECT *
FROM {output_dataset_id}.unioned_ehr_person AS p
'''.format(output_dataset_id=self.output_dataset_id)
person_response = bq_utils.query(q_person)
person_rows = bq_utils.response2rows(person_response)
q_observation = '''
SELECT *
FROM {output_dataset_id}.unioned_ehr_observation
WHERE observation_type_concept_id = 38000280
'''.format(output_dataset_id=self.output_dataset_id)
# observation should contain 4 records per person of type EHR
expected = len(person_rows) * 4
observation_response = bq_utils.query(q_observation)
observation_rows = bq_utils.response2rows(observation_response)
actual = len(observation_rows)
self.assertEqual(
actual, expected,
'Expected %s EHR person records in observation but found %s' %
(expected, actual))
def _create_drug_class_table(self):
table_name = 'drug_class'
fields = [{
"type": "integer",
"name": "concept_id",
"mode": "required"
}, {
"type": "string",
"name": "concept_name",
"mode": "required"
}, {
"type": "string",
"name": "drug_class_name",
"mode": "required"
}]
bq_utils.create_table(table_id=table_name,
fields=fields,
drop_existing=True,
dataset_id=self.bigquery_dataset_id)
bq_utils.query(q=main_constants.DRUG_CLASS_QUERY.format(
dataset_id=self.bigquery_dataset_id),
use_legacy_sql=False,
destination_table_id='drug_class',
retry_count=bq_consts.BQ_DEFAULT_RETRY_COUNT,
write_disposition='WRITE_TRUNCATE',
destination_dataset_id=self.bigquery_dataset_id)
def retraction_query_runner(queries):
query_job_ids = []
for query_dict in queries:
logger.debug('Retracting from %s.%s using query %s' %
(query_dict[DEST_DATASET], query_dict[DEST_TABLE],
query_dict[QUERY]))
if query_dict[DELETE_FLAG]:
job_results = bq_utils.query(q=query_dict[QUERY], batch=True)
rows_affected = job_results['numDmlAffectedRows']
logger.debug('%s rows deleted from %s.%s' %
(rows_affected, query_dict[DEST_DATASET],
query_dict[DEST_TABLE]))
else:
job_results = bq_utils.query(
q=query_dict[QUERY],
destination_table_id=query_dict[DEST_TABLE],
write_disposition=WRITE_TRUNCATE,
destination_dataset_id=query_dict[DEST_DATASET],
batch=True)
query_job_id = job_results['jobReference']['jobId']
query_job_ids.append(query_job_id)
incomplete_jobs = bq_utils.wait_on_jobs(query_job_ids)
if incomplete_jobs:
logger.debug('Failed on {count} job ids {ids}'.format(
count=len(incomplete_jobs), ids=incomplete_jobs))
logger.debug('Terminating retraction')
raise bq_utils.BigQueryJobWaitError(incomplete_jobs)
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):
# 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)
def test_merge_EHR(self, mock_check_cron):
self._load_datasets()
# enable exception propagation as described at https://goo.gl/LqDgnj
old_dataset_items = bq_utils.list_dataset_contents(
bq_utils.get_dataset_id())
expected_items = ['visit_id_mapping_table']
expected_items.extend(
['unioned_ehr_' + table_name for table_name in common.CDM_TABLES])
ehr_merge.merge(bq_utils.get_dataset_id(), self.project_id)
# check the result files were placed in bucket
dataset_items = bq_utils.list_dataset_contents(
bq_utils.get_dataset_id())
for table_name in common.CDM_TABLES:
cmd = 'SELECT COUNT(1) FROM unioned_ehr_{}'.format(table_name)
result = bq_utils.query(cmd)
self.assertEqual(
int(result['rows'][0]['f'][0]['v']),
2 * globals().get(table_name.upper() + '_COUNT', 0),
msg='failed for table unioned_ehr_{}'.format(table_name))
self.assertSetEqual(set(old_dataset_items + expected_items),
set(dataset_items))
table_name = 'condition_occurrence'
cmd_union = 'SELECT * FROM unioned_ehr_{}'.format(table_name)
cmd_pitt = 'SELECT * FROM pitt_{}'.format(table_name)
cmd_visit_mapping = "SELECT global_visit_id, mapping_visit_id FROM visit_id_mapping_table where hpo='pitt'"
qr_union = bq_utils.query(cmd_union)
qr_pitt = bq_utils.query(cmd_pitt)
qr_visit_mapping = bq_utils.query(cmd_visit_mapping)
union_result = query_result_to_payload(qr_union)
pitt_result = query_result_to_payload(qr_pitt)
visit_mapping_result = query_result_to_payload(qr_visit_mapping)
def get_element_from_list_of_lists(index, list_of_lists):
return [list_item[index] for list_item in list_of_lists]
for ind, pitt_visit_id in enumerate(
pitt_result['VISIT_OCCURRENCE_ID']):
if pitt_visit_id not in visit_mapping_result['MAPPING_VISIT_ID']:
continue
global_visit_id_index = visit_mapping_result[
'MAPPING_VISIT_ID'].index(pitt_visit_id)
global_visit_id = visit_mapping_result['GLOBAL_VISIT_ID'][
global_visit_id_index]
union_visit_id_index = union_result['VISIT_OCCURRENCE_ID'].index(
global_visit_id)
pitt_cols_without_id = [
values for key, values in pitt_result.items() if key not in
[u'VISIT_OCCURRENCE_ID', u'CONDITION_OCCURRENCE_ID']
]
union_cols_without_id = [
values for key, values in union_result.items() if key not in
[u'VISIT_OCCURRENCE_ID', u'CONDITION_OCCURRENCE_ID']
]
self.assertListEqual(
get_element_from_list_of_lists(ind, pitt_cols_without_id),
get_element_from_list_of_lists(union_visit_id_index,
union_cols_without_id))
def get_most_recent(app_id=None, drc_bucket=None, report_for=None):
"""
Query audit logs for paths to the most recent datasources.json files in the DRC bucket.
Note: Results are cached in a local json file to avoid unnecessary queries.
:param app_id: identifies the GCP project
:param drc_bucket: identifies the DRC bucket
:param report_for: denotes which query to use b/w achilles and results
:return: list of dict with keys `file_path`, `upload_timestamp`
"""
if app_id is None:
app_id = app_identity.get_application_id()
if drc_bucket is None:
drc_bucket = gcs_utils.get_drc_bucket()
if report_for == common.REPORT_FOR_ACHILLES:
if not os.path.exists(common.LATEST_REPORTS_JSON):
query = LATEST_REPORTS_QUERY.format(app_id=app_id, drc_bucket=drc_bucket, year=common.LOG_YEAR)
query_job = bq_utils.query(query)
result = bq_utils.response2rows(query_job)
with open(common.LATEST_REPORTS_JSON, 'w') as fp:
json.dump(result, fp, sort_keys=True, indent=4)
with open(common.LATEST_REPORTS_JSON, 'r') as fp:
return json.load(fp)
elif report_for == common.REPORT_FOR_RESULTS:
if not os.path.exists(common.LATEST_RESULTS_JSON):
query = LATEST_RESULTS_QUERY.format(app_id=app_id, drc_bucket=drc_bucket, year=common.LOG_YEAR)
query_job = bq_utils.query(query)
result = bq_utils.response2rows(query_job)
with open(common.LATEST_RESULTS_JSON, 'w') as fp:
json.dump(result, fp, sort_keys=True, indent=4)
with open(common.LATEST_RESULTS_JSON, 'r') as fp:
return json.load(fp)
def drop_concept_table(dataset_id):
if bq_utils.table_exists(common.CONCEPT):
q = "DROP TABLE {dataset}.concept;".format(dataset=dataset_id)
try:
bq_utils.query(q)
except HttpError as err:
if err.resp.status != 404:
raise
def load_analyses(hpo_id):
"""
Populate achilles lookup table
:param hpo_id:
:return:
"""
commands = _get_load_analysis_commands(hpo_id)
for command in commands:
bq_utils.query(command)
def test_ehr_person_to_observation(self, mock_tables_map):
# ehr person table converts to observation records
self._load_datasets()
mock_tables_map.return_value = [
common.OBSERVATION, common.LOCATION, common.CARE_SITE,
common.VISIT_OCCURRENCE
]
# perform ehr union
ehr_union.main(self.input_dataset_id, self.output_dataset_id,
self.project_id, self.hpo_ids)
person_query = '''
SELECT
person_id,
gender_concept_id,
gender_source_value,
race_concept_id,
race_source_value,
CAST(birth_datetime AS STRING) AS birth_datetime,
ethnicity_concept_id,
ethnicity_source_value,
EXTRACT(DATE FROM birth_datetime) AS birth_date
FROM {output_dataset_id}.unioned_ehr_person
'''.format(output_dataset_id=self.output_dataset_id)
person_response = bq_utils.query(person_query)
person_rows = bq_utils.response2rows(person_response)
# construct dicts of expected values
expected = []
for person_row in person_rows:
expected.extend(self.convert_ehr_person_to_observation(person_row))
# query for observation table records
query = '''
SELECT person_id,
observation_concept_id,
value_as_concept_id,
value_as_string,
observation_source_value,
observation_date
FROM {output_dataset_id}.unioned_ehr_observation AS obs
WHERE obs.observation_concept_id IN ({gender_concept_id},{race_concept_id},{dob_concept_id},
{ethnicity_concept_id})
'''
obs_query = query.format(
output_dataset_id=self.output_dataset_id,
gender_concept_id=eu_constants.GENDER_CONCEPT_ID,
race_concept_id=eu_constants.RACE_CONCEPT_ID,
dob_concept_id=eu_constants.DOB_CONCEPT_ID,
ethnicity_concept_id=eu_constants.ETHNICITY_CONCEPT_ID)
obs_response = bq_utils.query(obs_query)
obs_rows = bq_utils.response2rows(obs_response)
actual = obs_rows
self.assertCountEqual(expected, actual)
def test_integration_queries_to_retract_from_fake_dataset(self, mock_list_datasets, mock_is_ehr_dataset):
mock_list_datasets.return_value = [{'id': self.project_id+':'+self.bq_dataset_id}]
mock_is_ehr_dataset.return_value = True
job_ids = []
row_count_queries = {}
# load the cdm files into dataset
for cdm_file in test_util.NYC_FIVE_PERSONS_FILES:
cdm_file_name = os.path.basename(cdm_file)
cdm_table = cdm_file_name.split('.')[0]
hpo_table = bq_utils.get_table_id(self.hpo_id, cdm_table)
# store query for checking number of rows to delete
row_count_queries[hpo_table] = EXPECTED_ROWS_QUERY.format(dataset_id=self.bq_dataset_id,
table_id=hpo_table,
pids=retract_data_bq.int_list_to_bq(
self.person_ids))
retract_data_bq.logger.debug('Preparing to load table %s.%s' % (self.bq_dataset_id,
hpo_table))
with open(cdm_file, 'rb') as f:
gcs_utils.upload_object(gcs_utils.get_hpo_bucket(self.hpo_id), cdm_file_name, f)
result = bq_utils.load_cdm_csv(self.hpo_id, cdm_table, dataset_id=self.bq_dataset_id)
retract_data_bq.logger.debug('Loading table %s.%s' % (self.bq_dataset_id,
hpo_table))
job_id = result['jobReference']['jobId']
job_ids.append(job_id)
incomplete_jobs = bq_utils.wait_on_jobs(job_ids)
self.assertEqual(len(incomplete_jobs), 0, 'NYC five person load job did not complete')
retract_data_bq.logger.debug('All tables loaded successfully')
# use query results to count number of expected row deletions
expected_row_count = {}
for table in row_count_queries:
result = bq_utils.query(row_count_queries[table])
expected_row_count[table] = retract_data_bq.to_int(result['totalRows'])
# separate check to find number of actual deleted rows
q = TABLE_ROWS_QUERY.format(dataset_id=self.bq_dataset_id)
q_result = bq_utils.query(q)
result = bq_utils.response2rows(q_result)
row_count_before_retraction = {}
for row in result:
row_count_before_retraction[row['table_id']] = row['row_count']
deid_flag = False
# perform retraction
retract_data_bq.run_retraction(self.test_project_id, self.person_ids, self.hpo_id, deid_flag)
# find actual deleted rows
q_result = bq_utils.query(q)
result = bq_utils.response2rows(q_result)
row_count_after_retraction = {}
for row in result:
row_count_after_retraction[row['table_id']] = row['row_count']
for table in expected_row_count:
self.assertEqual(expected_row_count[table],
row_count_before_retraction[table] - row_count_after_retraction[table])
def test_get_lab_concept_summary_query(self):
summary_query = required_labs.get_lab_concept_summary_query(
FAKE_HPO_ID)
summary_response = bq_utils.query(summary_query)
summary_rows = bq_utils.response2rows(summary_response)
submitted_labs = [
row for row in summary_rows
if row['measurement_concept_id_exists'] == 1
]
actual_total_labs = summary_response['totalRows']
# Count the total number of labs required, this number should be equal to the total number of rows in the
# results generated by get_lab_concept_summary_query including the submitted and missing labs.
unique_ancestor_concept_query = sql_wrangle.qualify_tables(
"""SELECT DISTINCT ancestor_concept_id FROM `{project_id}.{dataset_id}.{table_id}`"""
.format(project_id=self.project_id,
dataset_id=self.dataset_id,
table_id=MEASUREMENT_CONCEPT_SETS_DESCENDANTS_TABLE))
unique_ancestor_cocnept_response = bq_utils.query(
unique_ancestor_concept_query)
expected_total_labs = unique_ancestor_cocnept_response['totalRows']
# Count the number of labs in the measurement table, this number should be equal to the number of labs
# submitted by the fake site
unique_measurement_concept_id_query = '''
SELECT
DISTINCT c.ancestor_concept_id
FROM
`{project_id}.{dataset_id}.{measurement_concept_sets_descendants}` AS c
JOIN
`{project_id}.{dataset_id}.{measurement}` AS m
ON
c.descendant_concept_id = m.measurement_concept_id
'''.format(project_id=self.project_id,
dataset_id=self.dataset_id,
measurement_concept_sets_descendants=
MEASUREMENT_CONCEPT_SETS_DESCENDANTS_TABLE,
measurement=bq_utils.get_table_id(
FAKE_HPO_ID, common.MEASUREMENT))
unique_measurement_concept_id_response = bq_utils.query(
unique_measurement_concept_id_query)
unique_measurement_concept_id_total_labs = unique_measurement_concept_id_response[
'totalRows']
self.assertEqual(int(expected_total_labs),
int(actual_total_labs),
msg='Compare the total number of labs')
self.assertEqual(int(unique_measurement_concept_id_total_labs),
len(submitted_labs),
msg='Compare the number '
'of labs submitted '
'in the measurement')
def test_execute_queries(self):
gender_nonbinary_concept_id = 1585841
gender_nonbinary_source_concept_id = 123
sex_female_concept_id = 1585847
sex_female_source_concept_id = 45878463
for tmpl in INSERT_FAKE_PARTICIPANTS_TMPLS:
query = tmpl.render(
project_id=self.project_id,
dataset_id=self.dataset_id,
gender_concept_id=repopulate_person_post_deid.GENDER_CONCEPT_ID,
gender_nonbinary_concept_id=gender_nonbinary_concept_id,
gender_nonbinary_source_concept_id=
gender_nonbinary_source_concept_id,
sex_at_birth_concept_id=repopulate_person_post_deid.
SEX_AT_BIRTH_CONCEPT_ID,
sex_female_concept_id=sex_female_concept_id,
sex_female_source_concept_id=sex_female_source_concept_id)
try:
resp = bq_utils.query(query)
except HttpError as e:
self.fail("failed to execute query '{}': {}".format(
query, e.content))
self.assertTrue(resp["jobComplete"])
clean_cdr_engine.clean_dataset(
self.project_id, self.dataset_id, self.sandbox_dataset_id,
[(repopulate_person_post_deid.
get_repopulate_person_post_deid_queries,)])
rows = bq_utils.response2rows(
bq_utils.query("SELECT * FROM `{}.{}.person`".format(
self.project_id, self.dataset_id)))
self.assertEquals(len(rows), 2)
by_participant = {r["person_id"]: r for r in rows}
self.assertPersonFields(
by_participant[1], {
"gender_concept_id": gender_nonbinary_concept_id,
"gender_source_value": "nonbinary_src",
"gender_source_concept_id": gender_nonbinary_source_concept_id,
"sex_at_birth_concept_id": sex_female_concept_id,
"sex_at_birth_source_value": "female_src",
"sex_at_birth_source_concept_id": sex_female_source_concept_id
})
self.assertPersonFields(
by_participant[2], {
"gender_concept_id": 0,
"gender_source_value": "No matching concept",
"gender_source_concept_id": 0,
"sex_at_birth_concept_id": 0,
"sex_at_birth_source_value": "No matching concept",
"sex_at_birth_source_concept_id": 0
})
def tearDown(self):
test_util.delete_all_tables(self.dataset_id)
# Delete concept table
drop_concept_table(self.dataset_id)
# re create concept table
q = """CREATE or REPLACE table `{project}.{dataset}.concept` as (
SELECT * FROM `{project}.{vocab}.concept`)""".format(
project=self.project_id,
dataset=self.dataset_id,
vocab=common.VOCABULARY_DATASET)
bq_utils.query(q)
def drop_or_truncate_table(command):
"""
Deletes or truncates table
:param command: query to run
:return: None
"""
if 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)
else:
table_id = sql_wrangle.get_drop_table_name(command)
bq_utils.delete_table(table_id)
def copy_metadata_table(project_id, source_dataset_id, target_dataset_id,
table_fields):
"""
:param project_id:
:param source_dataset_id:
:param target_dataset_id:
:param table_fields:
:return:
"""
create_metadata_table(target_dataset_id, table_fields)
query = COPY_QUERY.format(project=project_id, datset=source_dataset_id)
bq_utils.query(query,
destination_dataset_id=target_dataset_id,
destination_table_id=METADATA_TABLE)
def test_load_ehr_observation(self):
hpo_id = 'pitt'
dataset_id = self.dataset_id
table_id = bq_utils.get_table_id(hpo_id, table_name='observation')
q = 'SELECT observation_id FROM {dataset_id}.{table_id} ORDER BY observation_id'.format(
dataset_id=dataset_id, table_id=table_id)
expected_observation_ids = [
int(row['observation_id'])
for row in resources.csv_to_list(PITT_FIVE_PERSONS_OBSERVATION_CSV)
]
sc_bucket = self.client.get_bucket(gcs_utils.get_hpo_bucket(hpo_id))
bucket_blob = sc_bucket.blob('observation.csv')
with open(PITT_FIVE_PERSONS_OBSERVATION_CSV, 'rb') as fp:
bucket_blob.upload_from_file(fp)
result = bq_utils.load_cdm_csv(hpo_id, 'observation')
job_id = result['jobReference']['jobId']
incomplete_jobs = bq_utils.wait_on_jobs([job_id])
self.assertEqual(len(incomplete_jobs), 0,
'pitt_observation load job did not complete')
load_job_result = bq_utils.get_job_details(job_id)
load_job_result_status = load_job_result['status']
load_job_errors = load_job_result_status.get('errors')
self.assertIsNone(load_job_errors,
msg='pitt_observation load job failed: ' +
str(load_job_errors))
query_results_response = bq_utils.query(q)
query_job_errors = query_results_response.get('errors')
self.assertIsNone(query_job_errors)
actual_result = [
int(row['f'][0]['v']) for row in query_results_response['rows']
]
self.assertCountEqual(actual_result, expected_observation_ids)
def test_consented_person_id(self):
"""
Test observation data has seven (7) persons with consent records as described below
1: No
2: Yes
3: NULL
4: No followed by Yes
5: Yes followed by No
6: Yes followed by NULL
7: NULL and Yes with same date/time
"""
# sanity check
# pre-conditions
self.assertFalse(
bq_utils.table_exists(EHR_CONSENT_TABLE_ID,
self.combined_dataset_id))
# test
ehr_consent()
# post conditions
self.assertTrue(
bq_utils.table_exists(EHR_CONSENT_TABLE_ID,
self.combined_dataset_id),
'Table {dataset}.{table} created by consented_person'.format(
dataset=self.combined_dataset_id, table=EHR_CONSENT_TABLE_ID))
response = bq_utils.query('SELECT * FROM {dataset}.{table}'.format(
dataset=self.combined_dataset_id, table=EHR_CONSENT_TABLE_ID))
rows = bq_utils.response2rows(response)
expected = {2, 4}
actual = set(row['person_id'] for row in rows)
self.assertSetEqual(
expected, actual, 'Records in {dataset}.{table}'.format(
dataset=self.combined_dataset_id, table=EHR_CONSENT_TABLE_ID))
def _all_rdr_records_included(self):
"""
All rdr records are included whether or not there is corresponding ehr record
"""
for domain_table in DOMAIN_TABLES:
mapping_table = mapping_table_for(domain_table)
query = (
'SELECT rt.{domain_table}_id as id '
'FROM `{rdr_dataset_id}.{domain_table}` AS rt '
'LEFT JOIN `{combined_dataset_id}.{mapping_table}` AS m '
'ON rt.{domain_table}_id = m.src_{domain_table}_id '
'WHERE '
' m.{domain_table}_id IS NULL '
'OR NOT EXISTS '
' (SELECT 1 FROM `{combined_dataset_id}.{domain_table}` AS t '
' WHERE t.{domain_table}_id = m.{domain_table}_id)').format(
domain_table=domain_table,
rdr_dataset_id=bq_utils.get_rdr_dataset_id(),
combined_dataset_id=bq_utils.get_combined_dataset_id(),
mapping_table=mapping_table)
response = bq_utils.query(query)
rows = bq_utils.response2rows(response)
self.assertEqual(
0, len(rows),
"RDR records should map to records in mapping and combined tables"
)
def _ehr_only_records_excluded(self):
"""
EHR person records which are missing from RDR are excluded from combined
"""
query = ('WITH ehr_only AS '
' (SELECT person_id '
' FROM `{ehr_dataset_id}.person` AS ep '
' WHERE NOT EXISTS '
' (SELECT 1 '
' FROM `{rdr_dataset_id}.person` AS rp '
' WHERE rp.person_id = ep.person_id) '
' ) '
'SELECT '
'ehr_only.person_id AS ehr_person_id, '
'p.person_id AS combined_person_id '
'FROM ehr_only '
'LEFT JOIN `{combined_dataset_id}.person` AS p '
'ON ehr_only.person_id = p.person_id').format(
ehr_dataset_id=self.ehr_dataset_id,
rdr_dataset_id=self.rdr_dataset_id,
combined_dataset_id=self.combined_dataset_id)
response = bq_utils.query(query)
rows = bq_utils.response2rows(response)
self.assertGreater(len(rows), 0,
'Test data is missing EHR-only records')
for row in rows:
combined_person_id = row['combined_person_id']
self.assertIsNone(
combined_person_id,
'EHR-only person_id `{ehr_person_id}` found in combined when it should be excluded'
)
def test_copy_rdr_tables(self):
for table in RDR_TABLES_TO_COPY:
self.assertFalse(
bq_utils.table_exists(
table, self.combined_dataset_id)) # sanity check
copy_rdr_table(table)
actual = bq_utils.table_exists(table, self.combined_dataset_id)
self.assertTrue(
actual,
msg='RDR table {table} should be copied'.format(table=table))
# Check that row count in combined is same as rdr
query = (
'WITH rdr AS '
' (SELECT COUNT(1) n FROM `{rdr_dataset_id}.{table}`), '
'combined AS '
' (SELECT COUNT(1) n FROM `{combined_dataset_id}.{table}`) '
'SELECT '
'rdr.n AS rdr_count, '
'combined.n AS combined_count '
'FROM rdr, combined ').format(
rdr_dataset_id=self.rdr_dataset_id,
combined_dataset_id=self.combined_dataset_id,
table=table)
response = bq_utils.query(query)
rows = bq_utils.response2rows(response)
self.assertTrue(len(rows) == 1) # sanity check
row = rows[0]
rdr_count, combined_count = row['rdr_count'], row['combined_count']
msg_fmt = 'Table {table} has {rdr_count} in rdr and {combined_count} in combined (expected to be equal)'
self.assertEqual(
rdr_count, combined_count,
msg_fmt.format(table=table,
rdr_count=rdr_count,
combined_count=combined_count))
def _all_rdr_records_included(self):
"""
All rdr records are included whether or not there is corresponding ehr record
"""
for domain_table in DOMAIN_TABLES:
mapping_table = mapping_table_for(domain_table)
q = '''SELECT rt.{domain_table}_id as id
FROM {rdr_dataset_id}.{domain_table} rt
LEFT JOIN {ehr_rdr_dataset_id}.{mapping_table} m
ON rt.{domain_table}_id = m.src_{domain_table}_id
WHERE
m.{domain_table}_id IS NULL
OR NOT EXISTS
(SELECT 1 FROM {ehr_rdr_dataset_id}.{domain_table} t
WHERE t.{domain_table}_id = m.{domain_table}_id)'''.format(
domain_table=domain_table,
rdr_dataset_id=bq_utils.get_rdr_dataset_id(),
ehr_rdr_dataset_id=bq_utils.get_ehr_rdr_dataset_id(),
mapping_table=mapping_table)
response = bq_utils.query(q)
rows = test_util.response2rows(response)
self.assertEqual(
0, len(rows),
"RDR records should map to records in mapping and combined tables"
)
def export_from_path(p, hpo_id):
"""
Export results
:param p: path to SQL file
:param hpo_id: HPO to run export for
:return: `dict` structured for report render
"""
result = dict()
for f in list_files_only(p):
name = f[0:-4].upper()
abs_path = os.path.join(p, f)
with open(abs_path, 'r') as fp:
sql = fp.read()
sql = render(sql,
hpo_id,
results_schema=bq_utils.get_dataset_id(),
vocab_schema='')
query_result = bq_utils.query(sql)
# TODO reshape results
result[name] = query_result_to_payload(query_result)
for d in list_dirs_only(p):
abs_path = os.path.join(p, d)
name = d.upper()
# recursive call
dir_result = export_from_path(abs_path, hpo_id)
if name in result:
# a sql file generated the item already
result[name].update(dir_result)
else:
# add the item
result[name] = dir_result
return result
def query(q, dst_table_id, dst_dataset_id, write_disposition='WRITE_APPEND'):
"""
Run query and save results to a table
:param q: SQL statement
:param dst_table_id: save results in a table with the specified id
:param dst_dataset_id: identifies output dataset
:param write_disposition: WRITE_TRUNCATE, WRITE_EMPTY, or WRITE_APPEND (default, to preserve schema)
:return: query result
"""
query_job_result = bq_utils.query(q,
destination_table_id=dst_table_id,
destination_dataset_id=dst_dataset_id,
write_disposition=write_disposition)
query_job_id = query_job_result['jobReference']['jobId']
logging.info(f'Job {query_job_id} started for table {dst_table_id}')
job_status = query_job_result['status']
error_result = job_status.get('errorResult')
if error_result is not None:
msg = f'Job {query_job_id} failed because: {error_result}'
raise bq_utils.InvalidOperationError(msg)
incomplete_jobs = bq_utils.wait_on_jobs([query_job_id])
if len(incomplete_jobs) > 0:
raise bq_utils.BigQueryJobWaitError(incomplete_jobs)
return query_job_result
def test_load_csv(self):
from google.appengine.api import app_identity
app_id = app_identity.get_application_id()
table_name = 'achilles_analysis'
schema_file_name = table_name + '.json'
csv_file_name = table_name + '.csv'
schema_path = os.path.join(resources.fields_path, schema_file_name)
local_csv_path = os.path.join(test_util.TEST_DATA_EXPORT_PATH,
csv_file_name)
with open(local_csv_path, 'r') as fp:
response = gcs_utils.upload_object(self.hpo_bucket, csv_file_name,
fp)
hpo_bucket = self.hpo_bucket
gcs_object_path = 'gs://%(hpo_bucket)s/%(csv_file_name)s' % locals()
dataset_id = bq_utils.get_dataset_id()
load_results = bq_utils.load_csv(schema_path, gcs_object_path, app_id,
dataset_id, table_name)
load_job_id = load_results['jobReference']['jobId']
incomplete_jobs = bq_utils.wait_on_jobs([load_job_id])
self.assertEqual(len(incomplete_jobs), 0,
'loading table {} timed out'.format(table_name))
query_response = bq_utils.query('SELECT COUNT(1) FROM %(table_name)s' %
locals())
self.assertEqual(query_response['kind'], 'bigquery#queryResponse')
def test_integration_create_drug_route_mappings_table(self):
if bq_utils.table_exists(populate_route_ids.DRUG_ROUTES_TABLE_ID,
dataset_id=self.dataset_id):
bq_utils.delete_table(populate_route_ids.DRUG_ROUTES_TABLE_ID,
dataset_id=self.dataset_id)
if not bq_utils.table_exists(
populate_route_ids.DOSE_FORM_ROUTES_TABLE_ID,
dataset_id=self.dataset_id):
populate_route_ids.create_dose_form_route_mappings_table(
self.project_id, self.dataset_id)
populate_route_ids.create_drug_route_mappings_table(
self.project_id, self.dataset_id,
populate_route_ids.DOSE_FORM_ROUTES_TABLE_ID,
self.route_mapping_prefix)
time.sleep(10)
query = ("SELECT COUNT(*) AS n "
"FROM `{project_id}.{dataset_id}.{table_id}`").format(
project_id=self.project_id,
dataset_id=self.dataset_id,
table_id=populate_route_ids.DRUG_ROUTES_TABLE_ID)
result = bq_utils.query(query)
actual = bq_utils.response2rows(result)
self.assertGreater(actual[0]["n"], 0)
def _export_query_response_by_path(p, hpo_id):
"""Utility to create response test payloads"""
from validation import export
for f in export.list_files_only(p):
abs_path = os.path.join(p, f)
with open(abs_path, 'r') as fp:
sql = fp.read()
sql = export.render(sql,
hpo_id,
results_schema=bq_utils.get_dataset_id(),
vocab_schema='synpuf_100')
query_result = bq_utils.query(sql)
out_file = os.path.join(TEST_DATA_EXPORT_PATH,
f.replace('.sql', '_response.json'))
with open(out_file, 'w') as fp:
data = dict()
if 'rows' in query_result:
data['rows'] = query_result['rows']
if 'schema' in query_result:
data['schema'] = query_result['schema']
import json
json.dump(data,
fp,
sort_keys=True,
indent=4,
separators=(',', ': '))
def most_common_heel_errors(app_id=None, dataset_id=None, hpo_ids=None):
"""
:param app_id: Application Id
:param dataset_id: Dataset Id
:param hpo_ids: list of Hpo_ids
:return: None
"""
heel_errors = list()
if app_id is None:
app_id = app_identity.get_application_id()
if dataset_id is None:
dataset_id = bq_utils.get_dataset_id()
if not os.path.exists(HEEL_ERRORS_JSON) and not os.path.exists(
HEEL_ERRORS_CSV):
for hpo_id in hpo_ids:
if bq_utils.table_exists(
table_id='{hpo_id}_achilles_heel_results'.format(
hpo_id=hpo_id),
dataset_id=dataset_id):
query = heel_error_query.format(app_id=app_id,
dataset_id=dataset_id,
hpo_id=hpo_id)
query_job = bq_utils.query(query)
result = bq_utils.response2rows(query_job)
heel_errors.extend(result)
with open(HEEL_ERRORS_JSON, 'w') as fp:
json.dump(heel_errors, fp, sort_keys=True, indent=4)
parse_json_csv()
