clarity_to_csv_test.py
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import unittest
import clarity_to_csv as ctc
import pandas as pd
from unittest.mock import MagicMock
import sqlparse
#%%
testquerydir = 'C:\\Users\\LynchSe\\Documents\\Repos\\Covid19Related\\selah\\clarity_to_csv_tests\\'
testdatadir = 'C:\\Users\\LynchSe\\Documents\\Data\\clarity_to_csv_tests\\'
#TODO spin up a sqlite database here
def line_count(filename):
with open(filename) as myfile:
return len(myfile.readlines())
def remove_files(filenamelist):
import subprocess
for filename in filenamelist:
try:
subprocess.check_output('rm {}'.format(filename))
except Exception as e:
print(e)
pass
class TestStuff(unittest.TestCase):
def test_comment_with_semicolon(self):
sqltext = '''
SELECT TOP 2 PAT_ID FROM PAT_ENC;
/*
SELECT 1; SELECT 2;
*/
'''
genericcsvs = [
testdatadir + 'top2_pat_enc.csv'
]
remove_files(genericcsvs)
with ctc.get_clarity_engine().connect() as sqalconn:
ctc.clarity_to_csv_inner(sqltext, genericcsvs, sqalconn)
def test_none_csv(self):
sqlfilename = testquerydir + "testCohort.sql"
genericcsvs = [
None, #it should just skip this one
testdatadir + 'two_empis.csv',
]
remove_files(genericcsvs)
with ctc.get_clarity_engine().connect() as sqalconn:
ctc.clarity_to_csv(sqlfilename, genericcsvs, dbconn=sqalconn)
def integration_test(self):
sqlfilename1 = testquerydir + "testCohort.sql"
sqlfilename2 = testquerydir + "readTestCohort.sql"
genericcsvs = [
testdatadir + 'test1.csv',
testdatadir + 'test2.csv',
]
remove_files(genericcsvs)
with ctc.get_clarity_engine().connect() as sqalconn:
ctc.clarity_to_csv(sqlfilename1, genericcsvs, dbconn=sqalconn)
ctc.clarity_to_csv(sqlfilename2, genericcsvs, dbconn=sqalconn)
def unicode_error(self):
genericcsvs = [
testdatadir + 'test_cohort.csv'
]
remove_files(genericcsvs)
#I think it hangs if I don't include 'IF EXISTS'. GRRR... why??
sql_text = r'''
SELECT * FROM
X_COVID19_LAB_ORDERS l
WHERE PAT_ID IN ('055948350', '041356734', '057338121');
'''
with ctc.get_clarity_engine().connect() as conn:
ctc.clarity_to_csv_inner(sql_text, genericcsvs, conn)
def test_simple(self):
genericcsvs = [
testdatadir + 'test1.csv',
testdatadir + 'test2.csv'
]
remove_files(genericcsvs)
simple_sql_text = '''SELECT TOP 10 PAT_ID, PAT_ENC_CSN_ID FROM PAT_ENC;
SELECT TOP 5 CONTACT_DATE FROM PAT_ENC tablesample(0.01);
'''
with ctc.get_clarity_engine().connect() as conn:
ctc.clarity_to_csv_inner(simple_sql_text, genericcsvs, conn)
self.assertEqual(line_count( testdatadir + 'test1.csv'), 11)
self.assertEqual(line_count( testdatadir + 'test2.csv'), 6)
def test_wrapper(self):
sqlfilename = testquerydir + "tinyTestQuery.sql"
genericcsvs = [
testdatadir + 'test1.csv',
testdatadir + 'test2.csv',
testdatadir + 'test3.csv'
]
remove_files(genericcsvs)
ctc.clarity_to_csv(sqlfilename, genericcsvs)
#I believe this is hanging
def test_cohort(self):
genericcsvs = [
testdatadir + 'test_cohort.csv'
]
remove_files(genericcsvs)
#I think it hangs if I don't include 'IF EXISTS'. GRRR... why??
sql_text = '''
DROP TABLE IF EXISTS ##cohort;
CREATE TABLE ##cohort (EMPI VARCHAR(90) NOT NULL);
INSERT INTO ##cohort (EMPI) values ('8001111117'),('1000000000');
SELECT * FROM ##cohort;
'''
with ctc.get_clarity_engine().connect() as conn:
ctc.clarity_to_csv_inner(sql_text, genericcsvs, conn)
self.assertEqual(line_count(testdatadir + 'test_cohort.csv'), 3) #a header and two values
#TODO - deal with wrong number of csv's supplied
if __name__ == '__main__':
tests_to_run = [
"test_comment_with_semicolon"
# , "test_none_csv"
# , "integration_test"
# , "unicode_error"
# , "test_simple"
# , "test_wrapper"
# , "test_cohort"
]
suite = unittest.TestSuite()
for test in tests_to_run:
suite.addTest(TestStuff(test))
runner = unittest.TextTestRunner()
runner.run(suite)
# unittest.main()