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line would contain the id. If some other column contains the id,
use

    -c N

where N is the column (from 1) that contains the id.

This is a pipe command. The input is taken from the standard input, and the
output is to the standard output.

=head2 Related entities

The Compound entity has the following relationship links:

=over 4
    
=item HasUsage BiomassCompound

=item IsPresentIn Media

=item IsShownOn Diagram

=item IsTerminusFor Scenario

=item ParticipatesAs Reagent

=item UsesAliasForCompound Source


=back

=head2 Command-Line Options

=over 4

=item -c Column

Use the specified column to define the id of the entity to retrieve.

=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 label

=item abbr

=item msid

=item ubiquitous

=item mod_date

=item uncharged_formula

=item formula

=item mass

=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 = ( 'label', 'abbr', 'msid', 'ubiquitous', 'mod_date', 'uncharged_formula', 'formula', 'mass' );
my %all_fields = map { $_ => 1 } @all_fields;

my $usage = "usage: get_entity_Compound [-h] [-c column] [-a | -f field list] < ids > extended.by.a.column(s)";

my $column;
my $a;
my $f;
my $i = "-";
my @fields;
my $show_fields;
my $geO = Bio::KBase::CDMI::CDMIClient->new_get_entity_for_script('c=i'	   	=> \$column,
								  "a"	   	=> \$a,
								  "h"	   	=> \$show_fields,
								  "show-fields"	=> \$show_fields,
								  "fields=s" 	=> \$f,
								  'i=s'	   	=> \$i);
if ($show_fields)
{
    print STDERR "Available fields: @all_fields\n";
    exit 0;
}
if ($a && $f) { print STDERR $usage; exit 1 }
if ($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 "get_entity_Compound: unknown fields @err. Valid fields are: @all_fields\n";
	exit 1;
    }
} else {
    print STDERR $usage;
    exit 1;
}

my $ih;
if ($i eq '-')
{
    $ih = \*STDIN;
}
else
{
    open($ih, "<", $i) or die "Cannot open input file $i: $!\n";
}

while (my @tuples = Bio::KBase::Utilities::ScriptThing::GetBatch($ih, undef, $column)) {