Index: trunk/tools/rundiffskycell.pl
===================================================================
--- trunk/tools/rundiffskycell.pl	(revision 29141)
+++ trunk/tools/rundiffskycell.pl	(revision 29141)
@@ -0,0 +1,106 @@
+#!/bin/env perl
+
+# Run diff_skycell.pl for a previously run diff_skyfile.
+# The parameters are obtained from the diffSkyfile table database so it must not be reverted prior
+# to running this script.
+# if the --update argument is supplied we revert the diffSkyfile before running the command.
+# if --update is not supplied we simply re-run the command and leave the database unmodified.
+# WARNING: This script depends on the existing diff.skyfile.run task and diff_skycell.pl.
+# If they are changed this script may need to be modified
+#
+
+use strict;
+use warnings;
+use DBI;
+use IPC::Cmd 0.36 qw( can_run run );
+use PS::IPP::Metadata::Config;
+use PS::IPP::Config 1.01 qw( :standard );
+
+use Getopt::Long qw( GetOptions :config auto_help auto_version gnu_getopt );
+use Pod::Usage qw( pod2usage );
+use File::Basename;
+use IO::File;
+
+my ($first, $last, $stage, $alt_workdir, $no_verbose);
+
+my $dbname = "gpc1";
+my ($diff_id, $skycell_id, $threads, $update, $redirect);
+
+GetOptions(
+    'diff_id=i'         => \$diff_id,
+    'skycell_id=s'      => \$skycell_id,
+    'threads=i'         => \$threads,
+    'redirect-output'   => \$redirect,
+    'update'            => \$update,
+    'dbname=s'          => \$dbname,
+    'no-verbose'        => \$no_verbose, 
+) or pod2usage( 2 );
+
+pod2usage( -msg => "Unknown option: @ARGV", -exitval => 2 ) if @ARGV;
+pod2usage( -msg => "-diff_id and -skycell_id are required", -exitval => 2 )
+    if !$diff_id or !$skycell_id;
+
+my $ipprc =  PS::IPP::Config->new();
+my $dbh = getDBHandle();
+
+# find warp warp diffs that have a cleaned magicDSRun
+my $query1 = "SELECT path_base, diff_skyfile_id,bothways,reduction,diff_mode FROM diffRun JOIN diffSkyfile USING(diff_id)  JOIN diffInputSkyfile USING(diff_id, skycell_id) WHERE diff_id = $diff_id AND skycell_id = '$skycell_id'";
+
+my $stmt1 = $dbh->prepare($query1);
+$stmt1->execute();
+my $results = $stmt1->fetchrow_hashref();
+my $path_base = $results->{path_base};
+my $diff_skyfile_id = $results->{diff_skyfile_id};
+my $bothways = $results->{bothways};
+my $reduction = $results->{reduction};
+
+die "path_base not found\n" if !$path_base;
+die "diff_skyfile_id\n" if !$path_base;
+
+my $command = "diff_skycell.pl --diff_id $diff_id --skycell_id $skycell_id --diff_skyfile_id $diff_skyfile_id --outroot $path_base --run-state new";
+
+$command .= " --redirect-output" if $redirect;
+$command .= " --no-update" unless $update;
+$command .= " --verbose" unless $no_verbose;
+$command .= " --dbname $dbname" if $dbname;
+$command .= " --inverse" if $bothways;
+$command .= " --reduction $reduction" if $reduction;
+$command .= " --threads $threads" if $threads;
+
+print "command to process this skycell\n";
+print "$command\n";
+
+if ($update) {
+    my $revert_command = "difftool -revertdiffskyfile -diff_id $diff_id -skycell_id $skycell_id -dbname $dbname";
+    my $rc = system $revert_command;
+    if ($rc != 0) {
+        my $status = $rc >> 8;
+        print STDERR "$revert_command failed: $rc $status\n";
+        exit $status;
+    }
+}
+
+exit system $command;
+
+
+
+
+sub getDBHandle {
+    my $dbserver = metadataLookupStr($ipprc->{_siteConfig}, "DBSERVER");
+    my $dbuser = metadataLookupStr($ipprc->{_siteConfig}, "DBUSER");
+    my $dbpassword = metadataLookupStr($ipprc->{_siteConfig}, "DBPASSWORD");
+    if (!$dbname) {
+        $dbname = metadataLookupStr($ipprc->{_siteConfig}, "DBNAME");
+    }
+
+    die "database configuration set up" unless defined($dbserver) and defined($dbuser)
+        and defined($dbpassword) and defined($dbname);
+
+    my $dsn = "DBI:mysql:host=$dbserver;database=$dbname";
+
+    my $dbh = DBI->connect($dsn, $dbuser, $dbpassword) 
+        or die "Cannot connect to database.\n";
+
+    return $dbh;
+}
+