add regex for converting datetime_trunc calls to date_trunc

Author: Alistair Johnson

mimic-iv/concepts/convert_bigquery_to_postgres.sh

@@ -5,6 +5,7 @@
 export REGEX_SCHEMA='s/`physionet-data.(mimic_core|mimic_icu|mimic_derived|mimic_hosp).(.+?)`/\1.\2/g'
 # Note that these queries are very senstive to changes, e.g. adding whitespaces after comma can already change the behavior.
 export REGEX_DATETIME_DIFF="s/DATETIME_DIFF\((.+?),\s?(.+?),\s?(DAY|MINUTE|SECOND|HOUR|YEAR)\)/DATETIME_DIFF(\1,\2,'\3')/g"
+export REGEX_DATETIME_TRUNC="s/DATETIME_TRUNC\((.+?),\s?(DAY|MINUTE|SECOND|HOUR|YEAR)\)/DATE_TRUNC('\2', \1)/g"
 # Add necessary quotes to INTERVAL, e.g. "INTERVAL 5 hour" to "INTERVAL '5' hour"
 export REGEX_INTERVAL="s/interval\s([[:digit:]]+)\s(hour|day|month|year)/INTERVAL '\1' \2/gI"
 # Add numeric cast to ROUND(), e.g. "ROUND(1.234, 2)" to "ROUND( CAST(1.234 as numeric), 2)".
@@ -50,9 +51,9 @@ do
 
   # for two scripts, add a perl replace to cast rounded values as numeric
   if [[ "${tbl}" == "icustay_times" ]] || [[ "${tbl}" == "urine_output" ]]; then
-    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 "${REGEX_SCHEMA}" | sed -r -e "${REGEX_INTERVAL}" | sed -r -e "${REGEX_SECONDS}" | perl -0777 -pe "${PERL_REGEX_ROUND}" >> "postgres/${d}/${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 "${REGEX_INTERVAL}" | sed -r -e "${REGEX_SECONDS}" | perl -0777 -pe "${PERL_REGEX_ROUND}" >> "postgres/${d}/${tbl}.sql"
   else
-    cat "${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_SCHEMA}" | sed -r -e "${REGEX_INTERVAL}" | sed -r -e "${REGEX_SECONDS}" >> "postgres/${d}/${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 "${REGEX_INTERVAL}" | sed -r -e "${REGEX_SECONDS}" >> "postgres/${d}/${tbl}.sql"
   fi
 
   # write out a call to this script in the make concepts file
@@ -92,7 +93,7 @@ do
             echo -n " ${tbl} .."
             echo "-- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY." > "postgres/${d}/${tbl}.sql"
             echo "DROP TABLE IF EXISTS ${tbl}; CREATE TABLE ${tbl} AS " >> "postgres/${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_SCHEMA}" | sed -r -e "${REGEX_INTERVAL}" | perl -0777 -pe "${PERL_REGEX_ROUND}" >> "postgres/${d}/${fn}"
+            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 "${REGEX_INTERVAL}" | perl -0777 -pe "${PERL_REGEX_ROUND}" >> "postgres/${d}/${fn}"
 
             echo "\i ${d}/${fn}" >> postgres/postgres-make-concepts.sql
         fi
@@ -117,7 +118,7 @@ do
   echo "-- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY." > "postgres/${d}/${tbl}.sql"
   echo "DROP TABLE IF EXISTS ${tbl}; CREATE TABLE ${tbl} AS " >> "postgres/${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 "${REGEX_SCHEMA}" | sed -r -e "${REGEX_INTERVAL}" | sed -r -e "${REGEX_SECONDS}" >> "postgres/${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}" | sed -r -e "${REGEX_SECONDS}" >> "postgres/${d}/${tbl}.sql"
 
   # write out a call to this script in the make concepts file
   echo "\i ${d}/${tbl}.sql" >> postgres/postgres-make-concepts.sql