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#!perl
use strict;
use Data::Dumper;
use Carp;
#
# This is a SAS Component
#
HideShow 103 lines of Pod
=head1 get_relationship_IsCollectedInto
A genome belongs to only one genome set. For each set, this relationship marks the genome to be used as its representative.
Example:
    get_relationship_IsCollectedInto -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 OTU entity to return. Field-list is a comma-separated list of 
strings. The following fields are available:
=over 4
=item id
=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
=item representative
=back    
=item -to field-list
Choose a set of fields from the Genome entity to return. Field-list is a comma-separated list of 
strings. The following fields are available:
=over 4
=item id
=item pegs
=item rnas
=item scientific_name
=item complete
=item prokaryotic
=item dna_size
=item contigs
=item domain
=item genetic_code
=item gc_content
=item phenotype
=item md5
=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::Utilities::ScriptThing;
use Bio::KBase::CDMI::CDMIClient;
use Getopt::Long;
#Default fields
  
my @all_from_fields = ( 'id', 'pegs', 'rnas', 'scientific_name', 'complete', 'prokaryotic', 'dna_size', 'contigs', 'domain', 'genetic_code', 'gc_content', 'phenotype', 'md5', 'source_id' );
my @all_rel_fields = ( 'from_link', 'to_link', 'representative' );
my @all_to_fields = ( 'id',  );
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_IsCollectedInto [-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_IsCollectedInto(\@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_IsCollectedInto: unknown fields @err. Valid fields are @f\n";
                return 1;
        }
        return 0;
}