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fix: use sed -E for macOS/BSD sed compatibility #2058

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fix: use sed -E for macOS/BSD sed compatibility #2058

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7 changes: 4 additions & 3 deletions mimic-iii/concepts/convert_mimiciii_concepts_bq_to_psql.sh
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
#!/bin/bash
# This shell script converts BigQuery .sql files into PostgreSQL .sql files.
# Use sed -E (POSIX ERE) so the script works on both GNU and BSD sed (macOS).

# path in which we create the postgres concepts
TARGET_PATH='../concepts_postgres'
Expand Down Expand Up @@ -72,7 +73,7 @@ do
if ! [[ "$DIR_AND_TABLES_ALREADY_IN_PSQL" =~ "$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}/${d}/${tbl}.sql"
cat "${d}/${tbl}.sql" | sed -E -e "${REGEX_ARRAY}" | sed -E -e "${REGEX_HOUR_INTERVAL}" | sed -E -e "${REGEX_INT}" | sed -E -e "${REGEX_DATETIME_DIFF}" | sed -E -e "${REGEX_DATETIME_TRUNC}" | sed -E -e "${REGEX_SCHEMA}" | sed -E -e "${REGEX_INTERVAL}" >> "${TARGET_PATH}/${d}/${tbl}.sql"
fi

# write out a call to this script in the make concepts file
Expand Down Expand Up @@ -122,7 +123,7 @@ do
if ! [[ "$DIR_AND_TABLES_ALREADY_IN_PSQL" =~ "$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}"
cat "${d}/${tbl}.sql" | sed -E -e "${REGEX_ARRAY}" | sed -E -e "${REGEX_HOUR_INTERVAL}" | sed -E -e "${REGEX_INT}" | sed -E -e "${REGEX_DATETIME_DIFF}" | sed -E -e "${REGEX_DATETIME_TRUNC}" | sed -E -e "${REGEX_SCHEMA}" | sed -E -e "${REGEX_INTERVAL}" >> "${TARGET_PATH}/${d}/${fn}"
fi

# add statement to generate this table to make concepts script
Expand Down Expand Up @@ -150,7 +151,7 @@ do
if ! [[ "$DIR_AND_TABLES_ALREADY_IN_PSQL" =~ "$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}/${d}/${tbl}.sql"
cat "${d}/${tbl}.sql" | sed -E -e "${REGEX_ARRAY}" | sed -E -e "${REGEX_HOUR_INTERVAL}" | sed -E -e "${REGEX_INT}" | sed -E -e "${REGEX_DATETIME_DIFF}" | sed -E -e "${REGEX_DATETIME_TRUNC}" | sed -E -e "${REGEX_SCHEMA}" | sed -E -e "${REGEX_INTERVAL}" >> "${TARGET_PATH}/${d}/${tbl}.sql"
fi
# write out a call to this script in the make concepts file
echo "\i ${d}/${tbl}.sql" >> $TARGET_PATH/postgres-make-concepts.sql
Expand Down
2 changes: 1 addition & 1 deletion mimic-iv-ed/buildmimic/duckdb/import_duckdb.sh
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Expand Up @@ -74,7 +74,7 @@ fi
export REGEX_TIMESTAMP='s/TIMESTAMP\([0-9]+\)/TIMESTAMP/g'

# use sed + above regex to create tables within db
sed -r -e "${REGEX_TIMESTAMP}" ../postgres/create.sql |
sed -E -e "${REGEX_TIMESTAMP}" ../postgres/create.sql |
duckdb "$OUTFILE"

# goal: get path from find, e.g., ./1.0/icu/d_items
Expand Down
2 changes: 1 addition & 1 deletion mimic-iv-note/buildmimic/duckdb/import_duckdb.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -77,7 +77,7 @@ MIMIC_DIR=${MIMIC_DIR%/}
export REGEX_TIMESTAMP='s/TIMESTAMP\([0-9]+\)/TIMESTAMP/g'

# use sed + above regex to create tables within db
sed -r -e "${REGEX_TIMESTAMP}" ../postgres/create.sql | \
sed -E -e "${REGEX_TIMESTAMP}" ../postgres/create.sql | \
duckdb "$OUTFILE"

# goal: get path from find, e.g., ./1.0/icu/d_items
Expand Down
6 changes: 3 additions & 3 deletions mimic-iv/buildmimic/duckdb/import_duckdb.sh
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Expand Up @@ -80,9 +80,9 @@ export REGEX_SPEC_TYPE='s/spec_type_desc(.+)NOT NULL/spec_type_desc\1/g'
export REGEX_DRUG='s/drug +(VARCHAR.+)NOT NULL/drug \1/g'

# use sed + above regex to create tables within db
sed -r -e "${REGEX_TIMESTAMP}" ../postgres/create.sql | \
sed -r -e "${REGEX_SPEC_TYPE}" | \
sed -r -e "${REGEX_DRUG}" | \
sed -E -e "${REGEX_TIMESTAMP}" ../postgres/create.sql | \
sed -E -e "${REGEX_SPEC_TYPE}" | \
sed -E -e "${REGEX_DRUG}" | \
duckdb "$OUTFILE"

# goal: get path from find, e.g., ./1.0/icu/d_items
Expand Down
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