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Revision 1.4 - (download) (as text) (annotate)
Mon Dec 5 18:56:37 2005 UTC (14 years, 3 months ago) by olson
Branch: MAIN
CVS Tags: mgrast_dev_08112011, rast_rel_2009_05_18, mgrast_dev_08022011, rast_rel_2014_0912, rast_rel_2008_06_18, myrast_rel40, rast_rel_2008_06_16, mgrast_dev_05262011, 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, mgrast_dev_02212011, rast_rel_2010_1206, caBIG-05Apr06-00, 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, mgrast_dev_02222011, caBIG-13Feb06-00, rast_rel_2009_03_26, mgrast_dev_10262011, rast_rel_2008_11_24, rast_rel_2008_08_07, HEAD
Changes since 1.3: +17 -0 lines
Add license words.

#
# 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.
#

#
# Initialize a peg-based job scheduler. This uses the
# SEED database to store the jobs.
#
# Usage: init_peg_job_scheduler table-name input_gen_script organisms
#

use strict;
use FIG;
use Cluster;

if (@ARGV < 3)
{
    die "Usage: $0 job-table input_gen_script org-list \n";
}

my($table, $input_gen_script, @orgs) = @ARGV;

my $fig = new FIG;
my $jobmgr = new Cluster::DBJobMgr($fig, $table);

my $table = $jobmgr->table_name;
my $db = $jobmgr->db;

if (!$db->table_exists("peg_jobs"))
{
    $db->create_table(tbl => 'peg_jobs',
		      flds => qq(job_table varchar(64),
				 input_script text));
}

$db->drop_table(tbl => $table);
$db->create_table(tbl => $table,
		  flds => qq(peg varchar(32),
			     input text,
			     status int,
			     worker text,
			     job_taken timestamp,
			     job_finished timestamp,
			     output text));

$db->SQL("delete from peg_jobs where job_table = ?", undef, $table);
$db->SQL("insert into peg_jobs values (?, ?)", undef, $table, $input_gen_script);

#
# For transactions to work right, mysql needs the table to be
# of type InnoDB.
#

if ($jobmgr->dbms eq "mysql")
{
    $db->SQL("alter table $table  type = InnoDB");
}

my $tmp = "/tmp/pegs.$$";

open(TMP, ">$tmp");
			     
for my $org (@orgs)
{
    my @pegs = $fig->pegs_of($org);
    for my $peg (@pegs)
    {
	print TMP join("\t", $peg, '\N', Cluster::DBJobMgr::AVAIL, '\N', '\N', '\N', '\N'), "\n";
    }
}

close(TMP);

$db->load_table(file => $tmp, tbl => $table);
print "Loaded from $tmp\n";

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