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

#
# This is a SAS Component
#


=head1 all_entities_ObservationalUnit

Return all instances of the ObservationalUnit entity.

An ObservationalUnit is an individual plant that 1) is part of an experiment or study, 2) has measured traits, and 3) is assayed for the purpose of determining alleles.  

Example:

    all_entities_ObservationalUnit -a 

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

=head2 Related entities

The ObservationalUnit entity has the following relationship links:

=over 4
    
=item DefinedBy TaxonomicGrouping

=item HasTrait Trait

=item IsLocated Locality

=item IsPartOf StudyExperiment

=item IsVariedIn Contig

=item UsesReference Genome


=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_name

=item source_name2

=item plant_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_name', 'source_name2', 'plant_id' );
my %all_fields = map { $_ => 1 } @all_fields;

my $usage = "usage: all_entities_ObservationalUnit [-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_ObservationalUnit: unknown fields @err. Valid fields are: @all_fields\n";
	exit 1;
    }
}

my $start = 0;
my $count = 1_000_000;

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

while (%$h)
{
    while (my($k, $v) = each %$h)
    {
	print join("\t", $k, map { ref($_) eq 'ARRAY' ? join(",", @$_) : $_ } @$v{@fields}), "\n";
    }
    $start += $count;
    $h = $geO->all_entities_ObservationalUnit($start, $count, \@fields);
}
