[Bio] View of /Sprout/SetGroup.pl

Revision 1.2 - (download) (as text) (annotate)
Tue Feb 5 05:47:32 2008 UTC (11 years, 10 months ago) by parrello
Branch: MAIN
CVS Tags: mgrast_dev_08112011, mgrast_dev_08022011, rast_rel_2014_0912, rast_rel_2008_06_18, rast_rel_2008_06_16, rast_rel_2008_12_18, mgrast_dev_04082011, rast_rel_2008_07_21, rast_rel_2010_0928, rast_2008_0924, mgrast_version_3_2, mgrast_dev_12152011, rast_rel_2008_04_23, mgrast_dev_06072011, rast_rel_2008_09_30, rast_rel_2009_0925, rast_rel_2010_0526, rast_rel_2014_0729, rast_rel_2009_05_18, rast_rel_2010_1206, mgrast_release_3_0, mgrast_dev_03252011, rast_rel_2010_0118, mgrast_rel_2008_0924, mgrast_rel_2008_1110_v2, rast_rel_2009_02_05, rast_rel_2011_0119, mgrast_rel_2008_0625, mgrast_release_3_0_4, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_1, mgrast_dev_03312011, mgrast_release_3_1_2, mgrast_release_3_1_1, mgrast_release_3_1_0, mgrast_dev_04132011, rast_rel_2008_10_09, mgrast_dev_04012011, rast_release_2008_09_29, mgrast_rel_2008_0806, mgrast_rel_2008_0923, mgrast_rel_2008_0919, rast_rel_2009_07_09, rast_rel_2010_0827, mgrast_rel_2008_1110, myrast_33, rast_rel_2011_0928, rast_rel_2008_09_29, mgrast_rel_2008_0917, rast_rel_2008_10_29, mgrast_dev_04052011, rast_rel_2009_03_26, mgrast_dev_10262011, rast_rel_2008_11_24, rast_rel_2008_08_07, HEAD
Changes since 1.1: +0 -2 lines

Removed obsolete use clauses.

#!/usr/bin/perl -w

=head1 Set Primary Group

This script takes as parameters an NMPDR group name and a list of genome IDs and
updates the Sprout database to put the genomes into that group.

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 Cwd;
use File::Copy;
use File::Path;
use FIG;
use Sprout;
use SFXlate;

# Get the command-line options and parameters.
my ($options, @parameters) = StandardSetup([qw(Sprout) ],
                                           {
                                              phone => ["", "phone number (international format) to call when load finishes"],
                                           },
                                           "<groupName> <genome1> <genome2> ... <genomeN>",
                                           @ARGV);
# Set a variable to contain return type information.
my $rtype;
# Insure we catch errors.
eval {
    # Get the sprout database.
    my $sprout = SFXlate->new_sprout_only();
    # Save the group name.
    my $groupName = shift @parameters;
    # Loop through the genomes, doing the update.
    for my $genome (@parameters) {
        Trace("Converting $genome to $groupName.") if T(3);
        $sprout->UpdateEntity('Genome', $genome, { 'primary-group' => $groupName });
    }
    Trace("Processing complete.") if T(2);
};
if ($@) {
    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}, "Set Primary Group terminated with $rtype.");
    if ($msgID) {
        Trace("Phone message sent with ID $msgID.") if T(2);
    } else {
        Trace("Phone message not sent.") if T(2);
    }
}



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