From 572233c4bb529553b1e8c391a808c336192adafc Mon Sep 17 00:00:00 2001
From: Alistair Johnson <alistairewj@gmail.com>
Date: Thu, 23 Mar 2023 16:43:33 -0400
Subject: [PATCH] fix: bug where norepinephrine is skipped in output to psql

was due to a regex match succeeding against similarly named
norepinephrine_equivalent_dose. fix was to change to exact
matching with grep. re-ran to regenerate psql concepts.
fixed #1494
---
 mimic-iv/concepts/convert_bigquery_to_postgres.sh  | 14 ++++++++------
 .../medication/norepinephrine.sql                  |  4 +++-
 .../concepts_postgres/postgres-make-concepts.sql   |  1 +
 3 files changed, 12 insertions(+), 7 deletions(-)

diff --git a/mimic-iv/concepts/convert_bigquery_to_postgres.sh b/mimic-iv/concepts/convert_bigquery_to_postgres.sh
index fdf73dc95..6d5f4b0f5 100755
--- a/mimic-iv/concepts/convert_bigquery_to_postgres.sh
+++ b/mimic-iv/concepts/convert_bigquery_to_postgres.sh
@@ -126,22 +126,24 @@ do
             tbl="${fn%????}"
             echo -n " ${tbl} "
 
-            if [[ "$DIR_AND_TABLES_TO_PREBUILD" =~ "$d.$tbl" ]]; then
+            # check if var2 is in var1
+            if echo "$DIR_AND_TABLES_TO_PREBUILD" | grep -wq "$d.$tbl"; then
               echo -n "(prebuilt!) .."
               continue
-            elif [[ "$DIR_AND_TABLES_TO_SKIP" =~ "$d.$tbl" ]]; then
+            elif echo "$DIR_AND_TABLES_TO_SKIP" | grep -wq "$d.$tbl"; then
               echo -n "(skipping!) .."
               continue
-            else
-              echo -n ".."
             fi
 
             # re-write the script into psql using regex
             # the if statement ensures we do not overwrite tables which are already written in psql
-            if ! [[ "$DIR_AND_TABLES_ALREADY_IN_PSQL" =~ "$d.$tbl" ]]; then
+            if ! echo "$DIR_AND_TABLES_ALREADY_IN_PSQL" | grep -wq "$d.$tbl"; then
               echo "-- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY." > "${TARGET_PATH}/${d}/${tbl}.sql"
               echo "DROP TABLE IF EXISTS ${tbl}; CREATE TABLE ${tbl} AS" >> "${TARGET_PATH}/${d}/${tbl}.sql"
               cat "${d}/${tbl}.sql" | sed -r -e "${REGEX_ARRAY}" | sed -r -e "${REGEX_HOUR_INTERVAL}" | sed -r -e "${REGEX_INT}" | sed -r -e "${REGEX_DATETIME_DIFF}" | sed -r -e "${REGEX_DATETIME_TRUNC}" | sed -r -e "${REGEX_SCHEMA}" | sed -r -e "${REGEX_INTERVAL}" >> "${TARGET_PATH}/${d}/${fn}"
+              echo -n ".."
+            else
+              echo -n "(psql!) .."
             fi
             
             # add statement to generate this table
@@ -167,7 +169,7 @@ do
   
   # convert the bigquery script to psql and output it to the appropriate subfolder
   echo -n " ${d}.${tbl} .."
-  if ! [[ "$DIR_AND_TABLES_ALREADY_IN_PSQL" =~ "$d.$tbl" ]]; then
+  if ! echo "$DIR_AND_TABLES_ALREADY_IN_PSQL" | grep -wq "$d.$tbl"; then
     echo "-- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY." > "$TARGET_PATH/${d}/${tbl}.sql"
     echo "DROP TABLE IF EXISTS ${tbl}; CREATE TABLE ${tbl} AS" >> "$TARGET_PATH/${d}/${tbl}.sql"
 
diff --git a/mimic-iv/concepts_postgres/medication/norepinephrine.sql b/mimic-iv/concepts_postgres/medication/norepinephrine.sql
index 539d7a904..09b1e4dcf 100644
--- a/mimic-iv/concepts_postgres/medication/norepinephrine.sql
+++ b/mimic-iv/concepts_postgres/medication/norepinephrine.sql
@@ -1,10 +1,12 @@
 -- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
-DROP TABLE IF EXISTS norepinephrine; CREATE TABLE norepinephrine AS 
+DROP TABLE IF EXISTS norepinephrine; CREATE TABLE norepinephrine AS
 -- This query extracts dose+durations of norepinephrine administration
+-- Local hospital dosage guidance: 0.03 mcg/kg/min (low), 0.5 mcg/kg/min (high)
 SELECT
     stay_id, linkorderid
     -- two rows in mg/kg/min... rest in mcg/kg/min
     -- the rows in mg/kg/min are documented incorrectly
+    -- all rows converted into mcg/kg/min (equiv to ug/kg/min)
     , CASE WHEN rateuom = 'mg/kg/min' AND patientweight = 1 THEN rate
         -- below row is written for completion, but doesn't impact rows
         WHEN rateuom = 'mg/kg/min' THEN rate * 1000.0
diff --git a/mimic-iv/concepts_postgres/postgres-make-concepts.sql b/mimic-iv/concepts_postgres/postgres-make-concepts.sql
index e9b283c19..9c8b99fed 100644
--- a/mimic-iv/concepts_postgres/postgres-make-concepts.sql
+++ b/mimic-iv/concepts_postgres/postgres-make-concepts.sql
@@ -53,6 +53,7 @@ SET search_path TO mimiciv_derived, mimiciv_hosp, mimiciv_icu, mimiciv_ed;
 \i medication/epinephrine.sql
 \i medication/milrinone.sql
 \i medication/neuroblock.sql
+\i medication/norepinephrine.sql
 \i medication/phenylephrine.sql
 \i medication/vasopressin.sql