fixes for compatibility with mac os x sed and bash 3.x

Author: alistairewj

mimic-iv/concepts/convert_bigquery_to_postgres.sh

@@ -2,12 +2,12 @@
 # This shell script converts BigQuery .sql files into PostgreSQL .sql files.
 
 # String replacements are necessary for some queries.
-export REGEX_SCHEMA='s/`physionet-data.(mimic_core|mimic_icu|mimic_derived|mimic_hosp).(.+?)`/\1.\2/g'
+export REGEX_SCHEMA='s/`physionet-data.(mimiciv_hosp|mimiciv_icu|mimiciv_derived).([A-Za-z0-9_-]+)`/\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"
+export REGEX_DATETIME_DIFF="s/DATETIME_DIFF\(([^,]+), ?([^,]+), ?(DAY|MINUTE|SECOND|HOUR|YEAR)\)/DATETIME_DIFF(\1, \2, '\3')/g"
+export REGEX_DATETIME_TRUNC="s/DATETIME_TRUNC\(([^,]+), ?(DAY|MINUTE|SECOND|HOUR|YEAR)\)/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"
+export REGEX_INTERVAL="s/interval ([[:digit:]]+) (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)".
 export PERL_REGEX_ROUND='s/ROUND\(((.|\n)*?)\, /ROUND\( CAST\( \1 as numeric\)\,/g'
 # Specific queries for some problems that arose with some files.
@@ -83,7 +83,7 @@ do
         # only run SQL queries
         if [[ "${fn: -4}" == ".sql" ]]; then
             # table name is file name minus extension
-            tbl="${fn::-4}"
+            tbl="${fn%????}"
 
             # skip first_day_sofa as it depends on other firstday queries, we'll generate it later
             # we also skipped tables generated in the "Dependencies" loop above.