remove slash from filename

.travis.yml

@@ -20,7 +20,7 @@ python:
     - "2.7"
 
 before_script:
-  - psql -c 'create database mimic_test;' -U postgres
+  - psql -c 'create database MIMIC;' -U postgres
 
 # command to install dependencies
 install:

buildmimic/postgres/mimic_build_files/postgres_create_tables.sql

@@ -40,7 +40,8 @@ SET search_path TO mimiciii;
    as explained in the README file
 */
 
-  \set mimic_data_dir '/mimic_data'
+  -- include trailing slash
+  \set mimic_data_dir '/mimic_data/'
 
 --------------------------------------------------------
 --  DDL for Table ADMISSIONS
@@ -76,7 +77,7 @@ CREATE TABLE ADMISSIONS
 ALTER TABLE ADMISSIONS OWNER TO MIMIC;
 
 -- Example command for importing from a CSV to a table
-\set admissions_csv :mimic_data_dir '/ADMISSIONS_DATA_TABLE.csv'
+\set admissions_csv :mimic_data_dir 'ADMISSIONS_DATA_TABLE.csv'
 
 \COPY ADMISSIONS
     FROM :'admissions_csv'
@@ -117,7 +118,7 @@ CREATE TABLE CALLOUT
 
 ALTER TABLE CALLOUT OWNER TO MIMIC;
 
-\set callout_csv :mimic_data_dir '/CALLOUT_DATA_TABLE.csv'
+\set callout_csv :mimic_data_dir 'CALLOUT_DATA_TABLE.csv'
 
 \COPY CALLOUT
     FROM :'callout_csv'
@@ -139,7 +140,7 @@ ALTER TABLE CALLOUT OWNER TO MIMIC;
 
 ALTER TABLE CAREGIVERS OWNER TO MIMIC;
 
-\set caregivers_csv :mimic_data_dir '/CAREGIVERS_DATA_TABLE.csv'
+\set caregivers_csv :mimic_data_dir 'CAREGIVERS_DATA_TABLE.csv'
 
 -- Example command for importing from a CSV to a table
 \COPY CAREGIVERS
@@ -172,7 +173,7 @@ ALTER TABLE CAREGIVERS OWNER TO MIMIC;
 
 ALTER TABLE CHARTEVENTS OWNER TO MIMIC;
 
-\set chartevents_csv :mimic_data_dir '/CHARTEVENTS_DATA_TABLE.csv'
+\set chartevents_csv :mimic_data_dir 'CHARTEVENTS_DATA_TABLE.csv'
 
 -- Example command for importing from a CSV to a table
 \COPY CHARTEVENTS
@@ -202,7 +203,7 @@ ALTER TABLE CHARTEVENTS OWNER TO MIMIC;
 
 ALTER TABLE CPTEVENTS OWNER TO MIMIC;
 
-\set cptevents_csv :mimic_data_dir '/CPTEVENTS_DATA_TABLE.csv'
+\set cptevents_csv :mimic_data_dir 'CPTEVENTS_DATA_TABLE.csv'
 
 -- Example command for importing from a CSV to a table
 \COPY CPTEVENTS
@@ -234,7 +235,7 @@ ALTER TABLE CPTEVENTS OWNER TO MIMIC;
 
 ALTER TABLE DATETIMEEVENTS OWNER TO MIMIC;
 
-\set datetimeevents_csv :mimic_data_dir '/DATETIMEEVENTS_DATA_TABLE.csv'
+\set datetimeevents_csv :mimic_data_dir 'DATETIMEEVENTS_DATA_TABLE.csv'
 
 -- Example command for importing from a CSV to a table
 \COPY DATETIMEEVENTS
@@ -257,7 +258,7 @@ ALTER TABLE DATETIMEEVENTS OWNER TO MIMIC;
 
   ALTER TABLE DIAGNOSES_ICD OWNER TO MIMIC;
 
-\set diagnoses_icd_csv :mimic_data_dir '/DIAGNOSES_ICD_DATA_TABLE.csv'
+\set diagnoses_icd_csv :mimic_data_dir 'DIAGNOSES_ICD_DATA_TABLE.csv'
 
 -- Example command for importing from a CSV to a table
 \COPY DIAGNOSES_ICD
@@ -283,7 +284,7 @@ ALTER TABLE DATETIMEEVENTS OWNER TO MIMIC;
 
 ALTER TABLE DRGCODES OWNER TO MIMIC;
 
-\set drgcodes_csv :mimic_data_dir '/DRGCODES_DATA_TABLE.csv'
+\set drgcodes_csv :mimic_data_dir 'DRGCODES_DATA_TABLE.csv'
 
 -- Example command for importing from a CSV to a table
 \COPY DRGCODES
@@ -311,7 +312,7 @@ ALTER TABLE DRGCODES OWNER TO MIMIC;
 
 ALTER TABLE D_CPT OWNER TO MIMIC;
 
-\set d_cpt_csv :mimic_data_dir '/D_CPT_DATA_TABLE.csv'
+\set d_cpt_csv :mimic_data_dir 'D_CPT_DATA_TABLE.csv'
 
 -- Example command for importing from a CSV to a table
 \COPY D_CPT
@@ -334,7 +335,7 @@ ALTER TABLE D_CPT OWNER TO MIMIC;
 
 ALTER TABLE D_ICD_DIAGNOSES OWNER TO MIMIC;
 
-\set d_icd_diagnoses_csv :mimic_data_dir '/D_ICD_DIAGNOSES_DATA_TABLE.csv'
+\set d_icd_diagnoses_csv :mimic_data_dir 'D_ICD_DIAGNOSES_DATA_TABLE.csv'
 
 -- Example command for importing from a CSV to a table
 \COPY D_ICD_DIAGNOSES
@@ -357,7 +358,7 @@ ALTER TABLE D_ICD_DIAGNOSES OWNER TO MIMIC;
 
 ALTER TABLE D_ICD_PROCEDURES OWNER TO MIMIC;
 
-\set d_icd_procedures_csv :mimic_data_dir '/D_ICD_PROCEDURES_DATA_TABLE.csv'
+\set d_icd_procedures_csv :mimic_data_dir 'D_ICD_PROCEDURES_DATA_TABLE.csv'
 
 -- Example command for importing from a CSV to a table
 \COPY D_ICD_PROCEDURES
@@ -386,7 +387,7 @@ ALTER TABLE D_ICD_PROCEDURES OWNER TO MIMIC;
 
 ALTER TABLE D_ITEMS OWNER TO MIMIC;
 
-\set d_items_csv :mimic_data_dir '/D_ITEMS_DATA_TABLE.csv'
+\set d_items_csv :mimic_data_dir 'D_ITEMS_DATA_TABLE.csv'
 
 -- Example command for importing from a CSV to a table
 \COPY D_ITEMS
@@ -411,7 +412,7 @@ ALTER TABLE D_ITEMS OWNER TO MIMIC;
 
 ALTER TABLE D_LABITEMS OWNER TO MIMIC;
 
-\set d_labitems_csv :mimic_data_dir '/D_LABITEMS_DATA_TABLE.csv'
+\set d_labitems_csv :mimic_data_dir 'D_LABITEMS_DATA_TABLE.csv'
 
 -- Example command for importing from a CSV to a table
 \COPY D_LABITEMS
@@ -442,7 +443,7 @@ ALTER TABLE D_LABITEMS OWNER TO MIMIC;
 
 ALTER TABLE ICUSTAYS OWNER TO MIMIC;
 
-\set icustays_csv :mimic_data_dir '/ICUSTAYS_DATA_TABLE.csv'
+\set icustays_csv :mimic_data_dir 'ICUSTAYS_DATA_TABLE.csv'
 
 -- Example command for importing from a CSV to a table
 \COPY ICUSTAYS
@@ -483,7 +484,7 @@ ALTER TABLE ICUSTAYS OWNER TO MIMIC;
 
 ALTER TABLE INPUTEVENTS_CV OWNER TO MIMIC;
 
-\set inputevents_cv_csv :mimic_data_dir '/INPUTEVENTS_CV_DATA_TABLE.csv'
+\set inputevents_cv_csv :mimic_data_dir 'INPUTEVENTS_CV_DATA_TABLE.csv'
 
 -- Example command for importing from a CSV to a table
 \COPY INPUTEVENTS_CV
@@ -532,7 +533,7 @@ ALTER TABLE INPUTEVENTS_CV OWNER TO MIMIC;
 
 ALTER TABLE INPUTEVENTS_MV OWNER TO MIMIC;
 
-\set inputevents_mv_csv :mimic_data_dir '/INPUTEVENTS_MV_DATA_TABLE.csv'
+\set inputevents_mv_csv :mimic_data_dir 'INPUTEVENTS_MV_DATA_TABLE.csv'
 
 -- Example command for importing from a CSV to a table
 \COPY INPUTEVENTS_MV
@@ -559,7 +560,7 @@ ALTER TABLE INPUTEVENTS_MV OWNER TO MIMIC;
 
 ALTER TABLE LABEVENTS OWNER TO MIMIC;
 
-\set labevents_csv :mimic_data_dir '/LABEVENTS_DATA_TABLE.csv'
+\set labevents_csv :mimic_data_dir 'LABEVENTS_DATA_TABLE.csv'
 
 -- Example command for importing from a CSV to a table
 \COPY LABEVENTS
@@ -593,7 +594,7 @@ ALTER TABLE LABEVENTS OWNER TO MIMIC;
 
 ALTER TABLE MICROBIOLOGYEVENTS OWNER TO MIMIC;
 
-\set microbiologyevents_csv :mimic_data_dir '/MICROBIOLOGYEVENTS_DATA_TABLE.csv'
+\set microbiologyevents_csv :mimic_data_dir 'MICROBIOLOGYEVENTS_DATA_TABLE.csv'
 
 -- Example command for importing from a CSV to a table
 \COPY MICROBIOLOGYEVENTS
@@ -622,7 +623,7 @@ ALTER TABLE MICROBIOLOGYEVENTS OWNER TO MIMIC;
 
 ALTER TABLE NOTEEVENTS OWNER TO MIMIC;
 
-\set noteevents_csv :mimic_data_dir '/NOTEEVENTS_DATA_TABLE.csv'
+\set noteevents_csv :mimic_data_dir 'NOTEEVENTS_DATA_TABLE.csv'
 
 -- Example command for importing from a CSV to a table
 \COPY NOTEEVENTS
@@ -653,7 +654,7 @@ ALTER TABLE NOTEEVENTS OWNER TO MIMIC;
 
 ALTER TABLE OUTPUTEVENTS OWNER TO MIMIC;
 
-\set outputevents_csv :mimic_data_dir '/OUTPUTEVENTS_DATA_TABLE.csv'
+\set outputevents_csv :mimic_data_dir 'OUTPUTEVENTS_DATA_TABLE.csv'
 
 -- Example command for importing from a CSV to a table
 \COPY OUTPUTEVENTS
@@ -680,7 +681,7 @@ ALTER TABLE OUTPUTEVENTS OWNER TO MIMIC;
 
 ALTER TABLE PATIENTS OWNER TO MIMIC;
 
-\set patients_csv :mimic_data_dir '/PATIENTS_DATA_TABLE.csv'
+\set patients_csv :mimic_data_dir 'PATIENTS_DATA_TABLE.csv'
 
 -- Example command for importing from a CSV to a table
 \COPY PATIENTS
@@ -717,7 +718,7 @@ ALTER TABLE PATIENTS OWNER TO MIMIC;
 
 ALTER TABLE PRESCRIPTIONS OWNER TO MIMIC;
 
-\set prescriptions_csv :mimic_data_dir '/PRESCRIPTIONS_DATA_TABLE.csv'
+\set prescriptions_csv :mimic_data_dir 'PRESCRIPTIONS_DATA_TABLE.csv'
 
 -- Example command for importing from a CSV to a table
 \COPY PRESCRIPTIONS
@@ -761,7 +762,7 @@ ALTER TABLE PRESCRIPTIONS OWNER TO MIMIC;
 
 ALTER TABLE PROCEDUREEVENTS_MV OWNER TO MIMIC;
 
-\set procedureevents_mv_csv :mimic_data_dir '/PROCEDUREEVENTS_MV_DATA_TABLE.csv'
+\set procedureevents_mv_csv :mimic_data_dir 'PROCEDUREEVENTS_MV_DATA_TABLE.csv'
 
 -- Example command for importing from a CSV to a table
 \COPY PROCEDUREEVENTS_MV
@@ -784,7 +785,7 @@ ALTER TABLE PROCEDUREEVENTS_MV OWNER TO MIMIC;
 
 ALTER TABLE PROCEDURES_ICD OWNER TO MIMIC;
 
-\set procedures_icd_csv :mimic_data_dir '/PROCEDURES_ICD_DATA_TABLE.csv'
+\set procedures_icd_csv :mimic_data_dir 'PROCEDURES_ICD_DATA_TABLE.csv'
 
 -- Example command for importing from a CSV to a table
 \COPY PROCEDURES_ICD
@@ -808,7 +809,7 @@ ALTER TABLE PROCEDURES_ICD OWNER TO MIMIC;
 
 ALTER TABLE SERVICES OWNER TO MIMIC;
 
-\set services_csv :mimic_data_dir '/SERVICES_DATA_TABLE.csv'
+\set services_csv :mimic_data_dir 'SERVICES_DATA_TABLE.csv'
 
 -- Example command for importing from a CSV to a table
 \COPY SERVICES
@@ -839,7 +840,7 @@ ALTER TABLE SERVICES OWNER TO MIMIC;
 
 ALTER TABLE TRANSFERS OWNER TO MIMIC;
 
-\set transfers_csv :mimic_data_dir '/TRANSFERS_DATA_TABLE.csv'
+\set transfers_csv :mimic_data_dir 'TRANSFERS_DATA_TABLE.csv'
 
 -- Example command for importing from a CSV to a table
 \COPY TRANSFERS

buildmimic/tests/test_build.py

@@ -1,17 +1,55 @@
 import unittest
+import psycopg2
+
+conn = psycopg2.connect("dbname='MIMIC' user='postgres' host='localhost'")
+createdb_query = """
+CREATE USER MIMIC;
+CREATE DATABASE MIMIC OWNER MIMIC;
+\c MIMIC;
+CREATE SCHEMA MIMICIII;
+ALTER SCHEMA MIMICIII OWNER TO MIMIC;
+"""
+
+createdb = pd.read_sql_query(createdb_query,conn)
+
+test_query = """
+SELECT 'hello world'
+"""
+
+testq = pd.read_sql_query(test_query,conn)
 
 # Here's our "unit".
-def IsOdd(n):
+def isodd(n):
     return n % 2 == 1
 
+# 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
+
 # Here's our "unit tests".
-class IsOddTests(unittest.TestCase):
+class isoddtests(unittest.TestCase):
 
     def testOne(self):
-        self.failUnless(IsOdd(1))
+        self.failUnless(isodd(1))
 
     def testTwo(self):
-        self.failIf(IsOdd(2))
+        self.failIf(isodd(2))
 
 def main():
     unittest.main()