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reorder-csv.pl

Overview

reorder-csv.pl is a Perl utility that reorders the columns of an input CSV file to match the column order specified in a DDL file. The DDL can contain either a CREATE TABLE statement or index definitions, making it easier to prepare CSV files for database imports.

Features

  • DDL-Based Reordering: Extracts the column order from a DDL file (using either CREATE TABLE or CREATE INDEX statements).
  • Flexible Input/Output: Reads a CSV file with a header row and writes a new CSV with columns reordered according to the DDL.
  • Customizable Field Separator: Defaults to a tab (\t) but supports a custom separator.
  • Missing Columns Handling: Inserts a predefined NULL value (\N) for any columns missing from the input CSV.
  • Built-In Help: Displays usage information when required arguments are missing or when the help flag is used.

Dependencies

Note: If you installed omop-csv-validator this should work out-of-the-box.

  • Perl: Make sure Perl is installed on your system.
  • Modules:
    • Text::CSV_XS for CSV processing.

Usage

Run the script with the following options:

perl reorder-csv.pl -ddl-type postgresql --ddl DDL_FILE --input INPUT_CSV --output OUTPUT_CSV [--sep SEPARATOR]

Arguments

  • --ddl: File containing the DDL (either CREATE TABLE or index definitions).
  • --input: Input CSV file (must include a header row).
  • --output: Output CSV file with columns reordered to match the DDL.
  • --sep: (Optional) Field separator character (defaults to tab \t).
  • --table: (Optional) Override the table name to look up in the DDL. If not provided, the script derives it from the CSV filename.
  • --ddl-type: Type of the DDL format. Supported values: sqlite, postgresql (required).

Example

perl reorder-csv.pl --ddl schema_postgres.sql --ddl-type postgresql --input PERSON.csv --output reordered_data.csv --sep $'\t'
perl reorder-csv.pl --ddl schema_postgres.sql --ddl-type postgresql --input my_table.csv --output reordered_data.csv --sep $'\t' --table person

Author

Written by Manuel Rueda, PhD. Info about CNAG can be found at https://www.cnag.eu.

License

This project is released under the Artistic License 2.0.