#!perl
use strict;
use Data::Dumper;
use Carp;

#
# This is a SAS Component
#


=head1 all_entities_CoregulatedSet

Return all instances of the CoregulatedSet entity.

We need to represent sets of genes that are coregulated via some
regulatory mechanism.  In particular, we wish to represent genes
that are coregulated using transcription binding sites and
corresponding transcription regulatory proteins.
We represent a coregulated set (which may, or may not, be considered
an atomic regulon) using CoregulatedSet.


Example:

    all_entities_CoregulatedSet -a 

would retrieve all entities of type CoregulatedSet and include all fields
in the entities in the output.

=head2 Related entities

The CoregulatedSet entity has the following relationship links:

=over 4
    
=item IsBoundBy Feature

=item IsControlledUsing Feature

=item IsRegulatedSetOf Feature

=item WasFormulatedBy Source


=back


=head2 Command-Line Options

=over 4

=item -a

Return all fields.

=item -h

Display a list of the fields available for use.

=item -fields field-list

Choose a set of fields to return. Field-list is a comma-separated list of 
strings. The following fields are available:

=over 4

=item source_id

=back    
   
=back

=head2 Output Format

The standard output is a tab-delimited file. It consists of the input
file with an extra column added for each requested field.  Input lines that cannot
be extended are written to stderr.  

=cut

use Bio::KBase::CDMI::CDMIClient;
use Getopt::Long;

#Default fields

my @all_fields = ( 'source_id' );
my %all_fields = map { $_ => 1 } @all_fields;

my $usage = "usage: all_entities_CoregulatedSet [-show-fields] [-a | -f field list] > entity.data";

my $a;
my $f;
my @fields;
my $show_fields;
my $geO = Bio::KBase::CDMI::CDMIClient->new_get_entity_for_script("a" 		=> \$a,
								  "show-fields" => \$show_fields,
								  "h" 		=> \$show_fields,
								  "fields=s"    => \$f);

if ($show_fields)
{
    print STDERR "Available fields: @all_fields\n";
    exit 0;
}

if (@ARGV != 0 || ($a && $f))
{
    print STDERR $usage, "\n";
    exit 1;
}

if ($a)
{
    @fields = @all_fields;
}
elsif ($f) {
    my @err;
    for my $field (split(",", $f))
    {
	if (!$all_fields{$field})
	{
	    push(@err, $field);
	}
	else
	{
	    push(@fields, $field);
	}
    }
    if (@err)
    {
	print STDERR "all_entities_CoregulatedSet: unknown fields @err. Valid fields are: @all_fields\n";
	exit 1;
    }
}

my $start = 0;
my $count = 1000;

my $h = $geO->all_entities_CoregulatedSet($start, $count, \@fields );

while (%$h)
{
    while (my($k, $v) = each %$h)
    {
	print join("\t", $k, @$v{@fields}), "\n";
    }
    $start += $count;
    $h = $geO->all_entities_CoregulatedSet($start, $count, \@fields);
}
