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| import unittest | |
| import psycopg2 | |
| from psycopg2.extensions import ISOLATION_LEVEL_AUTOCOMMIT | |
| import pandas as pd | |
| import os | |
| from subprocess import call | |
| # Prep for Oracle and MySQL database connection | |
| # http://stackoverflow.com/questions/10065051/python-pandas-and-databases-like-mysql | |
| # import cx_Oracle | |
| # import MySQLdb | |
| # Config | |
| psqluser = 'postgres' | |
| testdbname = 'mimic_test_db' | |
| hostname = 'localhost' | |
| datadir = 'testdata/v1_3/' | |
| schema = 'mimiciii' | |
| # Set paths for scripts to be tested | |
| curpath = os.path.join(os.path.dirname(__file__)) + '/' | |
| # Display environment variables | |
| print(os.environ) | |
| # Create dictionary with table details for use in testing | |
| row_dict = { | |
| "ADMISSIONS": 58976, | |
| "CALLOUT": 34499, | |
| "CAREGIVERS": 7567, | |
| "CHARTEVENTS": 263201375, | |
| "CPTEVENTS": 573146, | |
| "D_CPT": 134, | |
| "D_ICD_DIAGNOSES": 14567, | |
| "D_ICD_PROCEDURES": 3882, | |
| "D_ITEMS": 12478, | |
| "D_LABITEMS": 755, | |
| "DATETIMEEVENTS": 4486049, | |
| "DIAGNOSES_ICD": 651047, | |
| "DRGCODES": 125557, | |
| "ICUSTAYS": 61532, | |
| "INPUTEVENTS_CV": 17528894, | |
| "INPUTEVENTS_MV": 3618991, | |
| "LABEVENTS": 27872575, | |
| "MICROBIOLOGYEVENTS": 328446, | |
| "NOTEEVENTS": 2078705, | |
| "OUTPUTEVENTS": 4349339, | |
| "PATIENTS": 46520, | |
| "PRESCRIPTIONS": 4156848, | |
| "PROCEDUREEVENTS_MV": 258066, | |
| "PROCEDURES_ICD": 240095, | |
| "SERVICES": 73343, | |
| "TRANSFERS": 261897 } | |
| # # Load build scripts | |
| # def executescripts(filename): | |
| # # Open and read the file as a single buffer | |
| # fd = open(filename, 'r') | |
| # sqlFile = fd.read() | |
| # fd.close() | |
| # # all SQL commands (split on ';') | |
| # sqlcommands = sqlFile.split(';') | |
| # # Execute every command from the input file | |
| # for command in sqlcommands: | |
| # # This will skip and report errors | |
| # # For example, if the tables do not yet exist, this will skip over | |
| # # the DROP TABLE commands | |
| # try: | |
| # c.execute(command) | |
| # except OperationalError, msg: | |
| # print "Command skipped: ", msg | |
| def run_postgres_build_scripts(cur): | |
| # Create tables | |
| fn = curpath + '../buildmimic/postgres/postgres_create_tables.sql' | |
| cur.execute(open(fn, "r").read()) | |
| # Loads data | |
| fn = curpath + '../buildmimic/postgres/postgres_load_data.sql' | |
| if os.environ.has_key('USER') and os.environ['USER'] == 'jenkins': | |
| # use full dataset | |
| mimic_data_dir = '/home/mimicadmin/data/mimiciii_1_3/' | |
| else: | |
| mimic_data_dir = curpath+datadir | |
| call(['psql','-f',fn,'-d',testdbname,'-U',psqluser,'-v','mimic_data_dir='+mimic_data_dir]) | |
| # Add constraints | |
| fn = curpath + '../buildmimic/postgres/postgres_add_constraints.sql' | |
| cur.execute(open(fn, "r").read()) | |
| # Add indexes | |
| fn = curpath + '../buildmimic/postgres/postgres_add_indexes.sql' | |
| cur.execute(open(fn, "r").read()) | |
| # # Prep for adding MySQL build | |
| # def run_mysql_build_scripts(cur): | |
| # # Create tables | |
| # fn = curpath + '../buildmimic/mysql/mysql_create_tables.sql' | |
| # cur.execute(open(fn, "r").read()) | |
| # # Loads data | |
| # fn = curpath + '../buildmimic/mysql/mysql_load_data.sql' | |
| # if os.environ.has_key('USER') and os.environ['USER'] == 'jenkins': | |
| # # use full dataset | |
| # mimic_data_dir = '/home/mimicadmin/data/mimiciii_1_3/' | |
| # else: | |
| # mimic_data_dir = curpath+datadir | |
| # call(['psql','-f',fn,'-d',testdbname,'-U',psqluser,'-v','mimic_data_dir='+mimic_data_dir]) | |
| # # Add constraints | |
| # fn = curpath + '../buildmimic/mysql/mysql_add_constraints.sql' | |
| # cur.execute(open(fn, "r").read()) | |
| # # Add indexes | |
| # fn = curpath + '../buildmimic/mysql/mysql_add_indexes.sql' | |
| # cur.execute(open(fn, "r").read()) | |
| # Class to run unit tests | |
| class test_postgres(unittest.TestCase): | |
| # setUpClass runs once for the class | |
| @classmethod | |
| def setUpClass(cls): | |
| # Connect to default postgres database | |
| cls.con = psycopg2.connect(dbname='postgres', user=psqluser) | |
| cls.con.set_isolation_level(ISOLATION_LEVEL_AUTOCOMMIT) | |
| cls.cur = cls.con.cursor() | |
| # Create test database | |
| try: | |
| cls.cur.execute('DROP DATABASE ' + testdbname) | |
| except psycopg2.ProgrammingError: | |
| pass | |
| cls.cur.execute('CREATE DATABASE ' + testdbname) | |
| cls.cur.close() | |
| cls.con.close() | |
| # Connect to the test database | |
| cls.con = psycopg2.connect(dbname=testdbname, user=psqluser) | |
| cls.con.set_isolation_level(ISOLATION_LEVEL_AUTOCOMMIT) | |
| cls.cur = cls.con.cursor() | |
| # Build the test database | |
| run_postgres_build_scripts(cls.cur) | |
| cls.cur.close() | |
| cls.con.close() | |
| # tearDownClass runs once for the class | |
| @classmethod | |
| def tearDownClass(cls): | |
| # Connect to default postgres database | |
| cls.con = psycopg2.connect(dbname='postgres', user=psqluser) | |
| cls.con.set_isolation_level(ISOLATION_LEVEL_AUTOCOMMIT) | |
| cls.cur = cls.con.cursor() | |
| # Drop test database | |
| cls.cur.execute('DROP DATABASE ' + testdbname) | |
| cls.cur.close() | |
| cls.con.close() | |
| # setUp runs once for each test method | |
| def setUp(self): | |
| # Connect to the test database | |
| self.con = psycopg2.connect(dbname=testdbname, user=psqluser) | |
| self.con.set_isolation_level(ISOLATION_LEVEL_AUTOCOMMIT) | |
| self.cur = self.con.cursor() | |
| # tearDown runs once for each test method | |
| def tearDown(self): | |
| self.cur.close() | |
| self.con.close() | |
| # The MIMIC test db has been created by this point | |
| # Add unit tests below | |
| def test_run_sample_query(self): | |
| test_query = """ | |
| SELECT 'hello world'; | |
| """ | |
| hello_world = pd.read_sql_query(test_query,self.con) | |
| self.assertEqual(hello_world.values[0][0],'hello world') | |
| def test_testddl(self): | |
| # Creates and drops an example schema and table | |
| fn = curpath + 'testddl.sql' | |
| self.cur.execute(open(fn, "r").read()) | |
| # self.assertEqual(1,1) | |
| # -------------------------------------------------- | |
| # Run a series of checks to ensure ITEMIDs are valid | |
| # All checks should return 0. | |
| # -------------------------------------------------- | |
| def test_itemids_in_inputevents_cv_are_shifted(self): | |
| query = """ | |
| -- prompt Number of ITEMIDs which were erroneously left as original value | |
| select count(*) from mimiciii.inputevents_cv | |
| where itemid < 30000; | |
| """ | |
| queryresult = pd.read_sql_query(query,self.con) | |
| self.assertEqual(queryresult.values[0][0],0) | |
| def test_itemids_in_inputevents_mv_are_shifted(self): | |
| query = """ | |
| -- prompt Number of ITEMIDs which were erroneously left as original value | |
| select count(*) from mimiciii.inputevents_mv | |
| where itemid < 220000; | |
| """ | |
| queryresult = pd.read_sql_query(query,self.con) | |
| self.assertEqual(queryresult.values[0][0],0) | |
| def test_itemids_in_outputevents_are_shifted(self): | |
| query = """ | |
| -- prompt Number of ITEMIDs which were erroneously left as original value | |
| select count(*) from mimiciii.outputevents | |
| where itemid < 30000; | |
| """ | |
| queryresult = pd.read_sql_query(query,self.con) | |
| self.assertEqual(queryresult.values[0][0],0) | |
| def test_itemids_in_inputevents_cv_are_in_range(self): | |
| query = """ | |
| -- prompt Number of ITEMIDs which are above the allowable range | |
| select count(*) from mimiciii.inputevents_cv | |
| where itemid > 50000; | |
| """ | |
| queryresult = pd.read_sql_query(query,self.con) | |
| self.assertEqual(queryresult.values[0][0],0) | |
| def test_itemids_in_outputevents_are_in_range(self): | |
| query = """ | |
| -- prompt Number of ITEMIDs which are not in the allowable range | |
| select count(*) from mimiciii.outputevents | |
| where itemid > 50000 and itemid < 220000; | |
| """ | |
| queryresult = pd.read_sql_query(query,self.con) | |
| self.assertEqual(queryresult.values[0][0],0) | |
| def test_itemids_in_chartevents_are_in_range(self): | |
| query = """ | |
| -- prompt Number of ITEMIDs which are not in the allowable range | |
| select count(*) from mimiciii.chartevents | |
| where itemid > 20000 AND itemid < 220000; | |
| """ | |
| queryresult = pd.read_sql_query(query,self.con) | |
| self.assertEqual(queryresult.values[0][0],0) | |
| def test_itemids_in_procedureevents_mv_are_in_range(self): | |
| query = """ | |
| -- prompt Number of ITEMIDs which are not in the allowable range | |
| select count(*) from mimiciii.procedureevents_mv | |
| where itemid < 220000; | |
| """ | |
| queryresult = pd.read_sql_query(query,self.con) | |
| self.assertEqual(queryresult.values[0][0],0) | |
| def test_itemids_in_labevents_are_in_range(self): | |
| query = """ | |
| -- prompt Number of ITEMIDs which are not in the allowable range | |
| select count(*) from mimiciii.labevents | |
| where itemid < 50000 or itemid > 60000; | |
| """ | |
| queryresult = pd.read_sql_query(query,self.con) | |
| self.assertEqual(queryresult.values[0][0],0) | |
| def test_itemids_in_microbiologyevents_are_in_range(self): | |
| query = """ | |
| -- prompt Number of ITEMIDs which are not in the allowable range | |
| select count(*) from mimiciii.microbiologyevents | |
| where SPEC_ITEMID < 70000 or SPEC_ITEMID > 80000 | |
| or ORG_ITEMID < 80000 or ORG_ITEMID > 90000 | |
| or AB_ITEMID < 90000 or AB_ITEMID > 100000; | |
| """ | |
| queryresult = pd.read_sql_query(query,self.con) | |
| self.assertEqual(queryresult.values[0][0],0) | |
| # ---------------------------------------------------- | |
| # RUN THE FOLLOWING TESTS ON THE FULL DATASET ONLY --- | |
| # ---------------------------------------------------- | |
| if os.environ.has_key('USER') and os.environ['USER'] == 'jenkins': | |
| def test_row_counts_are_as_expected(self): | |
| for tablename,expectedrows in row_dict.iteritems(): | |
| query = "SELECT COUNT(*) FROM " + schema + "." + tablename + ";" | |
| queryresult = pd.read_sql_query(query,self.con) | |
| self.assertEqual(queryresult.values[0][0],expectedrows) | |
| def test_age_and_los_is_expected(self): | |
| query = \ | |
| """ | |
| WITH icuadmissions as ( | |
| SELECT a.subject_id, a.hadm_id, i.icustay_id, | |
| a.admittime as hosp_admittime, a.dischtime as hosp_dischtime, | |
| i.first_careunit, | |
| DENSE_RANK() over(PARTITION BY a.hadm_id ORDER BY i.intime ASC) as icu_seq, | |
| p.dob, p.dod, i.intime as icu_intime, i.outtime as icu_outtime, | |
| i.los as icu_los, | |
| round((EXTRACT(EPOCH FROM (a.dischtime-a.admittime))/60/60/24) :: NUMERIC, 4) as hosp_los, | |
| p.gender, | |
| round((EXTRACT(EPOCH FROM (a.admittime-p.dob))/60/60/24/365.242) :: NUMERIC, 4) as age_hosp_in, | |
| round((EXTRACT(EPOCH FROM (i.intime-p.dob))/60/60/24/365.242) :: NUMERIC, 4) as age_icu_in, | |
| hospital_expire_flag, | |
| CASE WHEN p.dod IS NOT NULL | |
| AND p.dod >= i.intime - interval '6 hour' | |
| AND p.dod <= i.outtime + interval '6 hour' THEN 1 | |
| ELSE 0 END AS icu_expire_flag | |
| FROM admissions a | |
| INNER JOIN icustays i | |
| ON a.hadm_id = i.hadm_id | |
| INNER JOIN patients p | |
| ON a.subject_id = p.subject_id | |
| ORDER BY a.subject_id, i.intime) | |
| SELECT round(avg(age_icu_in)) as avg_age_icu, | |
| round(avg(hosp_los)) as avg_los_hosp, | |
| round(avg(icu_los)) as avg_los_icu | |
| FROM icuadmissions; | |
| """ | |
| queryresult = pd.read_sql_query(query,self.con) | |
| self.assertEqual(queryresult['avg_age_icu'].values[0][0],65) | |
| self.assertEqual(queryresult['avg_los_hosp'].values[0][0],11) | |
| self.assertEqual(queryresult['avg_los_icu'].values[0][0],5) | |
| def main(): | |
| unittest.main() | |
| if __name__ == '__main__': | |
| main() |