tangetools/transpose/transpose

#!/bin/bash

: <<=cut
=pod

=head1 NAME

transpose - transpose CSV file

=head1 SYNOPSIS

B<transpose> [-d I<delim>] [-b I<blocksize>] [I<input>]

=head1 DESCRIPTION

B<transpose> will read a CSV fie

=head1 OPTIONS

=over 9

=item I<input>

Input CSV file. If none is given reads from STDIN (standard input).


=item B<-d> I<delim>

Use I<delim> as delimiter in input and output.


=item B<-b> I<blocksize>

Pass chunks of I<blocksize> bytes to the internal transposer. Memory
usage will be 10 times I<blocksiz> per CPU core. Default is 10M.


=back


=head1 EXAMPLES

=head2 EXAMPLE: Transpose a medium sized TSV file

    cat medium.tsv | transpose -d '\t' > muidem.tsv

=head1 DESIGN

B<transpose> is designed to deal efficiently with medium sized data
(up to 30 TB per file) on systems with 100 MB RAM per CPU core. It
works by chopping the input into 10 MB blocks. Each block is
transposed in parallel and saved to disk. Then these files are pasted
together and finally removed.

=head1 REPORTING BUGS

Report bugs to <tange@gnu.org>.


=head1 AUTHOR

Copyright (C) 2013-2018 Ole Tange, http://ole.tange.dk and Free
Software Foundation, Inc.


=head1 LICENSE

Copyright (C) 2013 Free Software Foundation, Inc.

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 3 of the License, or
at your option any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <http://www.gnu.org/licenses/>.

=head2 Documentation license I

Permission is granted to copy, distribute and/or modify this documentation
under the terms of the GNU Free Documentation License, Version 1.3 or
any later version published by the Free Software Foundation; with no
Invariant Sections, with no Front-Cover Texts, and with no Back-Cover
Texts.  A copy of the license is included in the file fdl.txt.

=head2 Documentation license II

You are free:

=over 9

=item B<to Share>

to copy, distribute and transmit the work

=item B<to Remix>

to adapt the work

=back

Under the following conditions:

=over 9

=item B<Attribution>

You must attribute the work in the manner specified by the author or
licensor (but not in any way that suggests that they endorse you or
your use of the work).

=item B<Share Alike>

If you alter, transform, or build upon this work, you may distribute
the resulting work only under the same, similar or a compatible
license.

=back

With the understanding that:

=over 9

=item B<Waiver>

Any of the above conditions can be waived if you get permission from
the copyright holder.

=item B<Public Domain>

Where the work or any of its elements is in the public domain under
applicable law, that status is in no way affected by the license.

=item B<Other Rights>

In no way are any of the following rights affected by the license:

=over 2

=item *

Your fair dealing or fair use rights, or other applicable
copyright exceptions and limitations;

=item *

The author's moral rights;

=item *

Rights other persons may have either in the work itself or in
how the work is used, such as publicity or privacy rights.

=back

=back

=over 9

=item B<Notice>

For any reuse or distribution, you must make clear to others the
license terms of this work.

=back

A copy of the full license is included in the file as cc-by-sa.txt.

=head1 DEPENDENCIES

B<transpose> uses Perl, B<paste>, B<bash> and B<parallel>.


=head1 SEE ALSO

B<bash>(1), B<parallel>(1), B<paste>(1)

=cut


# transpose [-d delimiter] [-b blocksize] table.csv > transposed.csv
# cat table.csv | transpose [-d delimiter] [-b blocksize] > transposed.csv

transpose_inner() {
    # simple in-memory transpose
    # -d sep
    # Input:
    #   data to be transposed
    # Output:
    #   transposed data
    perl <(cat <<'cut-here-UbsAqi0j6GoOuk5W5yWA'
use Text::CSV;
use Getopt::Long;

Getopt::Long::Configure("bundling","require_order");
my $retval = GetOptions("debug|D=s" => \$opt::debug,
			"delimiter|d=s" => \$opt::delimiter,
			"verbose|v" => \@opt::verbose,
			"simple|s" => \$opt::simple,
    );

if(defined $opt::delimiter) {
    simple();
} else {
    die("-d must be set");
}

sub simple {
    my (@table);
    my $col = 0;
    my $csv_setting = { binary => 1, sep_char => $opt::delimiter };
    my $sep = $csv_setting->{sep_char};
    my $csv = Text::CSV->new($csv_setting)
	or die "Cannot use CSV: ".Text::CSV->error_diag ();

    while(my $l = <>) {
	if(not $csv->parse($l)) {
	    die "CSV has unexpected format";
	}
	# append to each row
	my $row = 0;
	for($csv->fields()) {
	    $table[$row][$col] = defined($_) ? $_ : '';
	    $row++;
	}
	$col++;
    }
    print map { join($sep,@$_),"\n" } @table;
}
cut-here-UbsAqi0j6GoOuk5W5yWA
	  ) "$@"
}
export -f transpose_inner

stdin_to_paste_files() {
    # Run transpose_inner on blocks from stdin
    # output each block as file name
    local block_size
    local sep
    block_size="$1"
    sep="$2"
    PARALLEL="-k --files --block $block_size" \
	    parallel --pipe transpose_inner -d "'$sep'"
}

file_to_paste_files() {
    # Run transpose_inner on blocks from $file
    # output each block as file name
    local block_size
    local sep
    block_size="$1"
    sep="$2"
    file="$3"
    PARALLEL="-k --files --block $block_size" \
	    parallel --pipe-part -a "$file" transpose_inner -d "'$sep'"
}

super_paste() {
    # Like 'paste' up to 1000000 files
    # More than 250000 files requires extra filehandles for GNU Parallel
    # The files are read from stdin
    local sep
    local paste_files
    local fifo

other_commands() {
    printf "\rSIGINT caught      "
    ls -l $paste_files
    cat $paste_files | parallel "eval rm -f {} $fifo{0#}"
    rm $paste_files
}

    trap 'other_commands' SIGINT

    sep="$1"
    paste_files=`tempfile`
    # basename
    fifo=`tempfile`
    rm $fifo
    # Group files from stdin in groups of 1000 files
    parallel -k -n1000 echo > $paste_files

    # Define replacement string {0#} to 0-pad job number
    export PARALLEL="--rpl "\''{0#} $f=1+int("".(log(total_jobs())/log(10)));
                    $_=sprintf("%0${f}d",seq())'\'

    # Make fifos that can be read from
    cat $paste_files | parallel "rm -f $fifo{0#}; mkfifo $fifo{0#}"

    # Start a paste process for every 1000 files
    cat $paste_files | parallel -j0 "eval paste -d \''$sep'\' {} > $fifo{0#}" &

    # Paste all the fifos
    eval paste -d "'$sep'" $fifo*

    # Cleanup
    cat $paste_files | parallel "eval rm -f {} $fifo{0#}"
    rm $paste_files
}

stdin_detect_sep() {
    # Read the first 3 lines and detect the separator
    # Save the read input to file
    local file
    file="$1"
    # TODO
    echo "$d"
}

usage() {
    echo "Usage: $0 [-d delimiter] [-b blocksize]" 1>&2; exit 1;
}

main() {
    block_size=10M
    while getopts ":b:d:" o; do
	case "${o}" in
	    d)
		d="$(printf "${OPTARG}")"
		if [ "'" = "${d}" ] ; then
		    echo "Delimiter cannot be '"
		    usage
		    exit
		fi
		;;
	    b)
		block_size="${OPTARG}"
		;;
	    *)
		usage
		;;
	esac
    done
    shift $((OPTIND-1))

    if [ -z "${d}" ] ; then
	d="$(printf "\t")"
    fi

    file="$@"
    first_lines=`tempfile`
    if [ -z "$file" ]; then
	sep="$(stdin_detect_sep $first_lines)"
	(cat $first_lines; rm $first_lines; cat) |
	    stdin_to_paste_files $block_size "$sep" | super_paste "$sep"
    else
	sep="$(stdin_detect_sep < "$file" $first_lines)"
	rm $first_lines
	file_to_paste_files $block_size "$sep" "$file" | super_paste "$sep"
    fi
}

# Make sure the whole file is read before starting
main "$@"