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#!perl
use strict;
use Data::Dumper;
use Carp;
#
# This is a SAS Component
#
HideShow 91 lines of Pod
=head1 query_entity_Pairing
Query the entity Pairing.
A pairing indicates that two features are found
close together in a genome. Not all possible pairings are stored in
the database; only those that are considered for some reason to be
significant for annotation purposes.The key of the pairing is the
concatenation of the feature IDs in alphabetical order with an
intervening colon.
Example:
    query_entity_Pairing -a 
=head2 Related entities
The Pairing entity has the following relationship links:
=over 4
     
=item Determines PairSet
=item IsPairOf Feature
=back
=head2 Command-Line Options
=over 4
=item -is field,value
Limit the results to entities where the given field has the given value.
=item -like field,value
Limit the results to entities where the given field is LIKE (in the sql sense) the given value.
=item -op operator,field,value
Limit the results to entities where the given field is related to the given value based on the given operator.
The operators supported are as follows. We provide text based alternatives to the comparison
operators so that extra quoting is not required to keep the command-line shell from 
confusing them with shell I/O redirection operators.
=over 4
=item < or lt
=item > or gt
=item <=  or le
=item >= or ge
=item =
=item LIKE
=back
=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
=back    
    
=back
=head2 Output Format
The standard output is a tab-delimited file containing a column
for each requested field.
=cut
use Bio::KBase::CDMI::CDMIClient;
use Getopt::Long;
#Default fields
my @all_fields = (  );
my %all_fields = map { $_ => 1 } @all_fields, 'id';
my $usage = "usage: query_entity_Pairing [-is field,value] [-like field,value] [-op operator,field,value] [-show-fields] [-a | -f field list] > entity.data";
my $a;
my $f;
my @fields;
my $show_fields;
my @query_is;
my @query_like;
my @query_op;
my %op_map = ('>', '>',
              'gt', '>',
              '<', '<',
              'lt', '<',
              '>=', '>=',
              'ge', '>=',
              '<=', '<=',
              'le', '<=',
              'like', 'LIKE',
              );
my $geO = Bio::KBase::CDMI::CDMIClient->new_get_entity_for_script("a"                => \$a,
                                                                  "show-fields" => \$show_fields,
                                                                  "h"           => \$show_fields,
                                                                  "is=s"        => \@query_is,
                                                                  "like=s"      => \@query_like,
                                                                  "op=s"        => \@query_op,
                                                                  "fields=s"    => \$f);
if ($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_Pairing: unknown fields @err. Valid fields are: @all_fields\n";
        exit 1;
    }
}
my @qry;
for my $ent (@query_is)
{
    my($field,$value) = split(/,/, $ent, 2);
    if (!$all_fields{$field})
    {
        die "$field is not a valid field\n";
    }
     
    push(@qry, [$field, '=', $value]);
}
for my $ent (@query_like)
{
    my($field,$value) = split(/,/, $ent, 2);
    if (!$all_fields{$field})
    {
        die "$field is not a valid field\n";
    }
     
    push(@qry, [$field, 'LIKE', $value]);
}
for my $ent (@query_op)
{
    my($op,$field,$value) = split(/,/, $ent, 3);
    if (!$all_fields{$field})
    {
        die "$field is not a valid field\n";
    }
    my $mapped_op = $op_map{lc($op)};
    if (!$mapped_op)
    {
        die "$op is not a valid operator\n";
    }
     
    push(@qry, [$field, $mapped_op, $value]);
}
my $h = $geO->query_entity_Pairing(\@qry, \@fields );
while (my($k, $v) = each %$h)
{
    print join("\t", $k, map { ref($_) eq 'ARRAY' ? join(",", @$_) : $_ } @$v{@fields}), "\n";
}