def main(self, argv):
"""Main method, callable from command line"""
log.setLevel(logging.FATAL)
usage_str = "usage: %prog [options]\n"
parser = OptionParser(usage=usage_str)
parser.add_option(
"-s",
"--startDate",
dest="startDate",
metavar="<startDate>",
help=
"Date string (e.g., 2011-12-15), if provided, will only run conversion on items with ordering time on or after this date."
)
parser.add_option(
"-e",
"--endDate",
dest="endDate",
metavar="<endDate>",
help=
"Date string (e.g., 2011-12-15), if provided, will only run conversion on items with ordering time before this date."
)
parser.add_option(
"-n",
"--normalizeMixtures",
dest="normalizeMixtures",
action="store_true",
help=
"If set, when find medication mixtures, will unravel / normalize into separate entries, one for each ingredient"
)
parser.add_option(
"-d",
"--doseCountLimit",
dest="doseCountLimit",
help=
"Medication orders with a finite number of doses specified less than this limit will be labeled as different items than those without a number specified, or whose number is >= to this limit. Intended to distinguish things like IV single bolus / use vs. continuous infusions and standing medication orders"
)
(options, args) = parser.parse_args(argv[1:])
log.info("Starting: " + str.join(" ", argv))
timer = time.time()
conv_options = ConversionOptions()
conv_options.extract_parser_options(options)
self.convertAndUpload(conv_options)
timer = time.time() - timer
log.info("%.3f seconds to complete", timer)
def setUp(self):
log.setLevel(logging.INFO) # without this no logs are printed
"""Prepare state for test cases"""
DBTestCase.setUp(self)
log.info("Sourcing from BigQuery DB")
ClinicalItemDataLoader.build_clinical_item_psql_schemata()
self.converter = STARRTreatmentTeamConversion.STARRTreatmentTeamConversion(
) # Instance to test on
self.bqConn = self.converter.bqConn
self.starrUtil = STARRUtil.StarrCommonUtils(self.converter.bqClient)
# point the converter to dummy source table
STARRTreatmentTeamConversion.SOURCE_TABLE = TEST_SOURCE_TABLE
def setUp(self):
"""Prepare state for test cases"""
log.setLevel(logging.INFO) # without this no logs are printed
DBTestCase.setUp(self)
ClinicalItemDataLoader.build_clinical_item_psql_schemata()
# point the converter to dummy source table
STARRDemographicsConversion.SOURCE_TABLE = TEST_SOURCE_TABLE
log.info("Generating test source data")
self.generate_test_and_expected_data(self.TEST_DATA_SIZE)
self.dump_test_data_to_csv(self.test_data_csv)
self.upload_test_data_csv_to_bigquery()
self.dump_patient_ids_to_test_to_csv(self.pat_id_csv)
def setUp(self):
log.setLevel(logging.INFO) # without this no logs are printed
"""Prepare state for test cases"""
DBTestCase.setUp(self)
log.info("Sourcing from BigQuery DB")
ClinicalItemDataLoader.build_clinical_item_psql_schemata()
self.converter = STARRTreatmentTeamConversion.STARRTreatmentTeamConversion(
) # Instance to test on
self.bqConn = self.converter.bqConn
self.starrUtil = STARRUtil.StarrCommonUtils(self.converter.bqClient)
# point the converter to dummy source table
STARRTreatmentTeamConversion.SOURCE_TABLE = TEST_SOURCE_TABLE
log.warn(
"Removing test table, if exists: {}".format(TEST_SOURCE_TABLE))
bq_cursor = self.bqConn.cursor()
bq_cursor.execute('DROP TABLE IF EXISTS {};'.format(TEST_SOURCE_TABLE))
def setUp(self):
"""Prepare state for test cases"""
log.setLevel(logging.INFO) # without this no logs are printed
DBTestCase.setUp(self)
ClinicalItemDataLoader.build_clinical_item_psql_schemata()
# point the converter to dummy source table
STARRDemographicsConversion.SOURCE_TABLE = TEST_SOURCE_TABLE
log.warn(
"Removing test table if it exists: {}".format(TEST_SOURCE_TABLE))
bq_cursor = self.bqConn.cursor()
bq_cursor.execute('DROP TABLE IF EXISTS {};'.format(TEST_SOURCE_TABLE))
log.info("Generating test source data")
self.generate_test_and_expected_data(self.TEST_DATA_SIZE)
self.starrUtil.dump_test_data_to_csv(self.header, self.test_data,
self.test_data_csv)
self.starrUtil.upload_csv_to_bigquery('starr_datalake2018',
'demographic', 'test_dataset',
'starr_demographic',
self.test_data_csv, self.header)
self.dump_patient_ids_to_test_to_csv(self.pat_id_csv)
where
pi.clinical_item_id = ci.clinical_item_id and
ci.clinical_item_category_id = cic.clinical_item_category_id and
cic.source_table = '%s'
order by
pi.external_id desc, ci.external_id desc
""" % (TEST_DEST_DATASET, TEST_DEST_DATASET, TEST_DEST_DATASET, TEST_SOURCE_TABLE)
bq_cursor = self.bqConn.cursor()
bq_cursor.execute(test_query)
actual_data = [list(row.values()) for row in bq_cursor.fetchall()]
log.debug('actual data: {}'.format(actual_data))
log.debug('expected data: {}'.format(self.expected_data))
self.assertEqualTable(self.expected_data, actual_data)
def suite():
"""Returns the suite of tests to run for this test class / module.
Use unittest.makeSuite methods which simply extracts all of the
methods for the given class whose name starts with "test"
"""
test_suite = unittest.TestSuite()
test_suite.addTest(unittest.makeSuite(TestSTARRTreatmentTeamConversion))
return test_suite
if __name__ == "__main__":
log.setLevel(logging.INFO) # without this no logs are printed
unittest.TextTestRunner(verbosity=RUNNER_VERBOSITY).run(suite())