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fix: escape quotes in duckdb COPY file paths #2086

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fix: escape quotes in duckdb COPY file paths #2086

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4 changes: 3 additions & 1 deletion mimic-iii/buildmimic/duckdb/import_duckdb.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -84,9 +84,11 @@ make_table_name () {
# load data into database
find "$MIMIC_DIR" -type f -regex '.*\.csv\(.gz\)*' | while IFS= read -r FILE; do
make_table_name "$FILE"
# escape single quotes for SQL string literal
FILE_SQL=${FILE//\'/\'\'}
echo "Loading $FILE .. \c"
try duckdb "$OUTFILE" <<-EOSQL
COPY $TABLE_NAME FROM '$FILE' (HEADER, DELIM ',', QUOTE '"', ESCAPE '"');
COPY $TABLE_NAME FROM '$FILE_SQL' (HEADER, DELIM ',', QUOTE '"', ESCAPE '"');
EOSQL
echo "done!"
done && echo "Successfully finished loading data into $OUTFILE."
4 changes: 3 additions & 1 deletion mimic-iv-ed/buildmimic/duckdb/import_duckdb.sh
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Expand Up @@ -95,6 +95,8 @@ make_table_name () {
# load data into database
find "$MIMIC_DIR" -type f -name '*.csv???' | sort | while IFS= read -r FILE; do
make_table_name "$FILE"
# escape single quotes for SQL string literal
FILE_SQL=${FILE//\'/\'\'}

# skip directories which we do not expect in mimic-iv-ed
# avoids syntax errors if mimic-iv in the same dir
Expand All @@ -104,7 +106,7 @@ find "$MIMIC_DIR" -type f -name '*.csv???' | sort | while IFS= read -r FILE; do
esac
echo "Loading $FILE .. "
try duckdb "$OUTFILE" <<-EOSQL
COPY $TABLE_NAME FROM '$FILE' (HEADER, DELIM ',', QUOTE '"', ESCAPE '"');
COPY $TABLE_NAME FROM '$FILE_SQL' (HEADER, DELIM ',', QUOTE '"', ESCAPE '"');
EOSQL
echo "done!"
done && echo "Successfully finished loading data into $OUTFILE."
4 changes: 3 additions & 1 deletion mimic-iv-note/buildmimic/duckdb/import_duckdb.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -98,6 +98,8 @@ make_table_name () {
# load data into database
find "$MIMIC_DIR" -type f -name '*.csv???' | sort | while IFS= read -r FILE; do
make_table_name "$FILE"
# escape single quotes for SQL string literal
FILE_SQL=${FILE//\'/\'\'}

# skip directories which we do not expect in mimic-iv-note
# avoids syntax errors if mimic-iv in the same dir
Expand All @@ -107,7 +109,7 @@ find "$MIMIC_DIR" -type f -name '*.csv???' | sort | while IFS= read -r FILE; do
esac
echo "Loading $FILE .."
OUTPUT=$(duckdb "$OUTFILE" 2>&1 <<-EOSQL
COPY $TABLE_NAME FROM '$FILE' (HEADER, DELIM ',', QUOTE '"', ESCAPE '"');
COPY $TABLE_NAME FROM '$FILE_SQL' (HEADER, DELIM ',', QUOTE '"', ESCAPE '"');
EOSQL
)
# If the table is missing in the DB, we emit a warning and continue.
Expand Down
4 changes: 3 additions & 1 deletion mimic-iv/buildmimic/duckdb/import_duckdb.sh
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -103,6 +103,8 @@ make_table_name () {
# load data into database
find "$MIMIC_DIR" -type f -name '*.csv???' | sort | while IFS= read -r FILE; do
make_table_name "$FILE"
# escape single quotes for SQL string literal
FILE_SQL=${FILE//\'/\'\'}

# skip directories which we do not expect in mimic-iv
# avoids syntax errors if mimic-iv-ed in the same dir
Expand All @@ -112,7 +114,7 @@ find "$MIMIC_DIR" -type f -name '*.csv???' | sort | while IFS= read -r FILE; do
esac
echo "Loading $FILE .. \c"
OUTPUT=$(duckdb "$OUTFILE" 2>&1 <<-EOSQL
COPY $TABLE_NAME FROM '$FILE' (HEADER, DELIM ',', QUOTE '"', ESCAPE '"');
COPY $TABLE_NAME FROM '$FILE_SQL' (HEADER, DELIM ',', QUOTE '"', ESCAPE '"');
EOSQL
)
# If the table is missing in the DB, we emit a warning and continue.
Expand Down
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