#!/usr/bin/perl -w

#
# Copyright (c) 2003-2006 University of Chicago and Fellowship
# for Interpretations of Genomes. All Rights Reserved.
#
# This file is part of the SEED Toolkit.
#
# The SEED Toolkit is free software. You can redistribute
# it and/or modify it under the terms of the SEED Toolkit
# Public License.
#
# You should have received a copy of the SEED Toolkit Public License
# along with this program; if not write to the University of Chicago
# at info@ci.uchicago.edu or the Fellowship for Interpretation of
# Genomes at veronika@thefig.info or download a copy from
# http://www.theseed.org/LICENSE.TXT.
#

=head1 NMPDR Status Checker

This script examines all of the genomes and displays the NMPDR group for each.

The currently-supported command-line options are as follows.

=over 4

=item user

Name suffix to be used for log files. If omitted, the PID is used.

=item trace

Numeric trace level. A higher trace level causes more messages to appear. The
default trace level is 2. Tracing will be directly to the standard output
as well as to a C<trace>I<User>C<.log> file in the FIG temporary directory,
where I<User> is the value of the B<user> option above.

=item sql

If specified, turns on tracing of SQL activity.

=item background

Save the standard and error output to files. The files will be created
in the FIG temporary directory and will be named C<err>I<User>C<.log> and
C<out>I<User>C<.log>, respectively, where I<User> is the value of the
B<user> option above.

=item h

Display this command's parameters and options.

=item phone

Phone number to message when the script is complete.

=back

=cut

use strict;
use Tracer;
use FIG;
use Cwd;
use File::Copy;
use File::Path;

# Get the command-line options and parameters.
my ($options, @parameters) = StandardSetup([qw(FIG) ],
                                           {
                                              phone => ["", "phone number (international format) to call when load finishes"],
                                           },
                                           "",
                                           @ARGV);
# Set a variable to contain return type information.
my $rtype;
# Insure we catch errors.
eval {
    # Get the FIG object.
    my $fig = FIG->new();
    # Get a list of all the genomes.
    my $genomes = $fig->genome_list();
    Trace(scalar(@{$genomes}) . " found.") if T(3);
    # Loop through the list.
    for my $genome (@{$genomes}) {
        # Get the genome ID and name.
        my ($genomeID, $genomeName) = @{$genome};
        # Only proceed if the genome is complete. Otherwise, it's not part of NMPDR.
        my $flag = $fig->is_complete($genomeID);
        Trace("Complete flag for $genomeID is $flag.") if T(4);
        if ($flag) {
            # Compute the NMPDR group.
            my $nmpdrFile = "$FIG_Config::organisms/$genomeID/NMPDR";
            if (-e $nmpdrFile) {
                # Get the NMPDR group from the file contents.
                my ($nmpdrGroup) = Tracer::GetFile($nmpdrFile);
                # Trace the result.
                Trace("$genomeID ($genomeName) = $nmpdrGroup") if T(2);
            }
        } else {
            # Denote this is not an NMPDR genome.
            Trace("$genomeID ($genomeName) not used.") if T(3);
        }
    }
    Trace("Processing complete.") if T(2);
};
if ($@) {
    Trace("Script failed with error: $@") if T(0);
    $rtype = "error";
} else {
    Trace("Script complete.") if T(2);
    $rtype = "no error";
}
if ($options->{phone}) {
    my $msgID = Tracer::SendSMS($options->{phone}, "NMPDR Status Checker terminated with $rtype.");
    if ($msgID) {
        Trace("Phone message sent with ID $msgID.") if T(2);
    } else {
        Trace("Phone message not sent.") if T(2);
    }
}

1;