Index: trunk/tools/runbgchip.pl
===================================================================
--- trunk/tools/runbgchip.pl	(revision 33068)
+++ trunk/tools/runbgchip.pl	(revision 33068)
@@ -0,0 +1,180 @@
+#!/bin/env perl
+
+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 $dbname = "gpc1";
+my ($chip_bg_id, $class_id, $threads, $update, $redirect, $pretend, $save_temps);
+
+my $zaplog;
+
+GetOptions(
+    'chip_bg_id=i'         => \$chip_bg_id,
+    'class_id=s'      => \$class_id,
+    'threads=i'         => \$threads,
+    'pretend'           => \$pretend,
+    'zaplog'            => \$zaplog,
+    'redirect-output'   => \$redirect,
+    'update'            => \$update,
+    'dbname=s'          => \$dbname,
+    'no-verbose'        => \$no_verbose, 
+    'save-temps'        => \$save_temps,
+) or pod2usage( 2 );
+
+pod2usage( -msg => "Unknown option: @ARGV", -exitval => 2 ) if @ARGV;
+pod2usage( -msg => "--chip_bg_id and --class_id are required", -exitval => 2 )
+    if !$chip_bg_id or !$class_id;
+
+my $ipprc =  PS::IPP::Config->new();
+my $dbh = getDBHandle();
+
+my $query1 = "SELECT chipBackgroundImfile.path_base, camera, exp_id, chipBackgroundImfile.fault, chipBackgroundRun.reduction, chipBackgroundRun.state";
+$query1 .= " FROM chipBackgroundRun join chipBackgroundImfile using(chip_bg_id) JOIN chipRun using(chip_id) JOIN rawExp using(exp_id) WHERE chip_bg_id = $chip_bg_id AND class_id = '$class_id'";
+
+my $stmt1 = $dbh->prepare($query1);
+$stmt1->execute();
+my $results = $stmt1->fetchrow_hashref();
+die "query returned no results\n" if !$results;
+my $path_base = $results->{path_base};
+my $reduction = $results->{reduction};
+my $camera = $results->{camera};
+my $state = $results->{state};
+my $fault = $results->{fault};
+my $deburned = $results->{deburned};
+my $exp_id = $results->{exp_id};
+
+die "cannot update database for a chip that is not faulted\n" if $update and !$fault;
+
+die "path_base not found\n" if !$path_base;
+die "camera not found\n" if !$camera;
+die "state not found\n" if !$state;
+
+my  $run_state;
+if ($state eq 'full' or $state eq 'new') {
+    $run_state = 'new';
+} elsif ($state eq 'update') {
+    $run_state = 'update';
+} else {
+    die "unexpected chipRun.state found: $state\n";
+}
+
+my $command = "background_chip.pl --chip_bg_id $chip_bg_id --class_id $class_id --camera $camera --outroot $path_base" ;
+
+$command .= " --reduction $reduction" if $reduction and ($reduction ne "NULL");
+$command .= " --redirect-output" if $redirect;
+$command .= " --save-temps" if $save_temps;
+$command .= " --no-update" unless $update;
+$command .= " --verbose" unless $no_verbose;
+$command .= " --dbname $dbname" if $dbname;
+
+if ($update) {
+    my $revert_command = "bgtool -revertchip -chip_bg_id $chip_bg_id -class_id $class_id -dbname $dbname";
+    if ($pretend) {
+        print "skipping $revert_command\n";
+    } else {
+        my $rc = system $revert_command;
+        if ($rc != 0) {
+            my $status = $rc >> 8;
+            print STDERR "$revert_command failed: $rc $status\n";
+            exit $status;
+        }
+    }
+}
+print "command to process this chip\n";
+print "$command\n";
+
+exit 0 if $pretend;
+
+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;
+}
+
+__END__
+
+=pod
+
+=head1 NAME
+
+runchipimfile.pl - gather the parameters for and execute chip_imfile.pl
+
+=head1 SYNOPSIS
+    
+    XXX: pod TODO
+
+    perl runwarpskyfile.pl --warp_id <warp_id> --skycell_id <skycell_id> [--threads <num_threads>] [--update] [--redirect-output] [--pretend] [--dbname <dbname>]
+
+Query the database for the results of a warp skycell and rerun the processing, optionally reverting a faulted
+run.
+
+=over 4
+
+=item * --warp_id <warp_id>
+
+The id of the warpSkyfile run to process.
+
+=item * --skycell_id <skycell_id>
+
+The skycell_id of the warpSkyfile run to process.
+
+=item * --threads <num_threads>
+
+The number of threads to use. Default 1.
+Optional.
+
+
+=item * --update
+
+Revert a faulted skycell before processing. If the skycell is not faulted no processing is done.
+WARNING: insure that the standard science procesing either has warp stage turned off or the
+label of this warpRun ommited from the list of labels otherwise it may attempt to processes this run at the same time.
+Optional.
+
+=item *  --redirect-output
+
+Send the output of the command to the logfile. (This is the default if --update is supplied).
+Optional.
+
+=item * --pretend
+
+Just print the commands that would be executed, but do not run them.
+Optional.
+
+=item * --dbname <dbname>
+
+Name of the IPP databse to query. Default is 'gpc1'.
+Optional.
+
+
+=head1 SEE ALSO
+L<runchipimfile.pl>, L<runcameraexp.pl>, L<rundiffskyfile.pl>
+
+=cut