Merge pull request #66 from mit2400/master

Solving build error by updating schema - "relation xxx does not exist"

SQL_Queries/codes.sql

@@ -1,8 +1,9 @@
+SET SEARCH_PATH TO public,mimiciii;
 SELECT
     i.icustay_id, d.subject_id, d.hadm_id,
     array_agg(d.icd9_code ORDER BY seq_num ASC) AS icd9_codes
-FROM mimiciii.diagnoses_icd d 
-    LEFT OUTER JOIN (SELECT ccs_matched_id, icd9_code from mimiciii.ccs_dx) c
+FROM diagnoses_icd d 
+    LEFT OUTER JOIN (SELECT ccs_matched_id, icd9_code from ccs_dx) c
     ON c.icd9_code = d.icd9_code
     INNER JOIN icustays i
     ON i.hadm_id = d.hadm_id AND i.subject_id = d.subject_id

SQL_Queries/debug_statics.sql

@@ -1,5 +1,5 @@
 \echo "This file is just for debugging"
-SET search_path TO mimiciii;
+SET search_path TO public,mimiciii;
 select distinct
     i.subject_id,
     i.hadm_id,

mimic_direct_extract.py

@@ -734,7 +734,7 @@ def plot_variable_histograms(col_names, df):
                     help='Postgres host. Try "/var/run/postgresql/" for Unix domain socket errors.')
     ap.add_argument('--psql_dbname', type=str, default='mimic',
                     help='Postgres database name.')
-    ap.add_argument('--psql_schema_name', type=str, default='mimiciii',
+    ap.add_argument('--psql_schema_name', type=str, default='public,mimiciii',
                     help='Postgres database name.')
     ap.add_argument('--psql_user', type=str, default=None,
                     help='Postgres user.')

mimic_querier.py

@@ -25,7 +25,7 @@ def __init__(
         self,
         exclusion_criteria_template_vars={},
         query_args={}, # passed wholesale to psycopg2.connect
-        schema_name='mimiciii'
+        schema_name='public,mimiciii'
     ):
         """ A class to facilitate repeated Queries to a MIMIC psql database """
         self.exclusion_criteria_template_vars = {}

utils/niv-durations.sql

@@ -4,7 +4,7 @@
 -- events can then be used for various purposes: calculating the total duration
 -- of mechanical ventilation, cross-checking values (e.g. PaO2:FiO2 on vent), etc
 
-SET SEARCH_PATH TO 'mimiciii';
+SET SEARCH_PATH TO public,mimiciii;
 
 -- The query's logic is roughly:
 --    1) The presence of a mechanical ventilation setting starts a new ventilation event

utils/setup_user_env.sh

@@ -10,7 +10,7 @@ mkdir -p $MIMIC_EXTRACT_OUTPUT_DIR
 
 export DBUSER=bnestor
 export DBNAME=mimic
-export SCHEMA=mimiciii
+export SCHEMA=public,mimiciii
 export HOST=mimic
 export DBSTRING="dbname=$DBNAME options=--search_path=$SCHEMA"
 alias psql="psql -h $HOST -U $DBUSER "