ega_csv2json: A script that parses EGA metadata files and serializes it to json/hash data structures.

ega_csv2json.pl -i <file.csv> [-options]

  Arguments:                       
    -i|input                       Metadata txt, csv or tsv file

  Options:
    -f|format                      Output format [>json|hash]
    -h|help                        Brief help message
    -man                           Full documentation
    -debug                         Print debugging (from 1 to 5, being 5 max)
    -verbose                       Verbosity on

To be defined.

ega_csv2json: A script that parses EGA metadata files and serializes it to json/hash data structures.

The script runs on Linux (tested on Debian-based distribution). Perl 5 is installed by default on Linux, but you might need to install a few CPAN modules.

First we install cpanminus (with sudo privileges):

$ sudo apt-get install cpanminus

Then the modules:

$ cpanm --sudo --installdeps .

If you prefer to install the CPAN modules in the directory of the application we recommend using the module Carton

$ cpanm --sudo Carton

And then execute this command:

$ carton install

For executing ega_csv2json you will need:

• Input file

  Uncompressed CSV, TSV, or TXT file.

  Please note that this script is a proof-of-concept and we are aware that it does not parse well all files (e.g., multivalue cells).

Examples:

$ ./ega_csv2json.pl -i file.csv > file.json

$ $path/ega_csv2json.pl -i file.csv -format hash > file.txt

$ carton exec -- ./ega_csv2json.pl -i file.csv > file.json # If using Carton

Written by Manuel Rueda, PhD. Info about EGA can be found at https://ega-archive.org/.

Report bugs or comments to [email protected].

This PERL file is copyrighted. See the LICENSE file included in this distribution.