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

#
# This is a SAS Component
#


=head1 query_entity_Reaction

Query the entity Reaction.

A reaction is a chemical process that converts one set of
compounds (substrate) to another set (products).

Example:

    query_entity_Reaction -a 

=head2 Related entities

The Reaction entity has the following relationship links:

=over 4
    
=item Involves Reagent

=item IsDisplayedOn Diagram

=item IsRequiredBy Requirement

=item IsUsedAs ReactionRule

=item ParticipatesIn Scenario

=item RunsByDefaultIn Compartment

=item UsesAliasForReaction Source


=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

=item mod_date

=item name

=item msid

=item abbr

=item equation

=item reversibility

=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 = ( 'mod_date', 'name', 'msid', 'abbr', 'equation', 'reversibility' );
my %all_fields = map { $_ => 1 } @all_fields, 'id';

my $usage = "usage: query_entity_Reaction [-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_Reaction: 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_Reaction(\@qry, \@fields );

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

