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

#
# This is a SAS Component
#


=head1 get_relationship_IsDefaultLocationOf

This relationship connects a reagent to the compartment
which is its default location during the reaction.

Example:

    get_relationship_IsDefaultLocationOf -a < ids > table.with.fields.added

would read in a file of ids and add a column for each field in the relationship.

The standard input should be a tab-separated table (i.e., each line
is a tab-separated set of fields).  Normally, the last field in each
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 Command-Line Options

=over 4

=item -c Column

This is used only if the column containing id is not the last.

=item -from field-list

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

=over 4

=item id

=item abbr

=item mod_date

=item name

=item msid

=back    

=item -rel field-list

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

=over 4

=item from_link

=item to_link

=back    

=item -to field-list

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

=over 4

=item id

=item stoichiometry

=item cofactor

=item compartment_index

=item transport_coefficient

=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::Utilities::ScriptThing;
use Bio::KBase::CDMI::CDMIClient;
use Getopt::Long;

#Default fields
 
my @all_from_fields = ( 'id', 'abbr', 'mod_date', 'name', 'msid' );
my @all_rel_fields = ( 'from_link', 'to_link',  );
my @all_to_fields = ( 'id', 'stoichiometry', 'cofactor', 'compartment_index', 'transport_coefficient' );

my %all_from_fields = map { $_ => 1 } @all_from_fields;
my %all_rel_fields = map { $_ => 1 } @all_rel_fields;
my %all_to_fields = map { $_ => 1 } @all_to_fields;

my @default_fields = ('from-link', 'to-link');

my @from_fields;
my @rel_fields;
my @to_fields;

my $usage = "usage: get_relationship_IsDefaultLocationOf [-c column] [-a | -from field list -rel field list -to field list] < ids > extended.by.a.column(s)\n";

my $column;
my $input_file;
my $a;
my $f;
my $r;
my $t;
my $h;
my $i = "-";

my $geO = Bio::KBase::CDMI::CDMIClient->new_get_entity_for_script("c=i"		=> \$column,
								  "h"	   	=> \$h,
								  "show-fields"	=> \$h,
								  "a"	   	=> \$a,
								  "from=s" 	=> \$f,
								  "rel=s" 	=> \$r,
								  "to=s" 	=> \$t,
								  'i=s'	   	=> \$i);

if ($h) {
	print STDERR "from: ", join(",", @all_from_fields), "\n";
	print STDERR "relation: ", join(",", @all_rel_fields), "\n";
	print STDERR "to: ", join(",", @all_to_fields), "\n";
	exit 0;
}

if ($a  && ($f || $r || $t)) {die $usage};

if ($a) {
	@from_fields = @all_from_fields;
	@rel_fields = @all_rel_fields;
	@to_fields = @all_to_fields;
} elsif ($f || $t || $r) {
	my $err = 0;
	if ($f) {
		@from_fields = split(",", $f);
		$err += check_fields(\@from_fields, %all_from_fields);
	}
	if ($r) {
		@rel_fields = split(",", $r);
		$err += check_fields(\@rel_fields, %all_rel_fields);
	}
	if ($t) {
		@to_fields = split(",", $t);
		$err += check_fields(\@to_fields, %all_to_fields);
	}
	if ($err) {exit 1;}	
} else {
	@rel_fields =  @default_fields;
}
 
my $ih;
if ($input_file)
{
    open $ih, "<", $input_file or die "Cannot open input file $input_file: $!";
}
else
{
    $ih = \*STDIN;
}


while (my @tuples = Bio::KBase::Utilities::ScriptThing::GetBatch($ih, undef, $column)) {
	
    my @h = map { $_->[0] } @tuples;
    my $h = $geO->get_relationship_IsDefaultLocationOf(\@h, \@from_fields, \@rel_fields, \@to_fields);
    my %results;
    for my $result (@$h) {
        my @from;
        my @rel;
        my @to;
        my $from_id;
        my $res = $result->[0];
	for my $key (@from_fields) {
		push (@from,$res->{$key});
	}
        $res = $result->[1];
	$from_id = $res->{'from_link'};
	for my $key (@rel_fields) {
		push (@rel,$res->{$key});
	}
	$res = $result->[2];
	for my $key (@to_fields) {
		push (@to,$res->{$key});
	}
        if ($from_id) {
	    push @{$results{$from_id}}, [@from, @rel, @to];
        }
    }
    for my $tuple (@tuples)
    {
	my($id, $line) = @$tuple;
	my $resultsForId = $results{$id};
	if ($resultsForId) {
	    for my $result (@$resultsForId) {
		print join("\t", $line, @$result) . "\n";
	    }
	}
    }
}

sub check_fields {
	my ($fields, %all_fields) = @_;
	my @err;
	for my $field (@$fields) {
		if (!$all_fields{$field})
		{
		    push(@err, $field);
		}
        }
	if (@err) {
		my @f = keys %all_fields;
		print STDERR "get_relationship_IsDefaultLocationOf: unknown fields @err. Valid fields are @f\n";
		return 1;
	}
	return 0;
}