Index: /trunk/ippScripts/scripts/chip_imfile.pl
===================================================================
--- /trunk/ippScripts/scripts/chip_imfile.pl	(revision 31940)
+++ /trunk/ippScripts/scripts/chip_imfile.pl	(revision 31941)
@@ -44,4 +44,7 @@
 my ( $exp_id, $chip_id, $class_id, $chip_imfile_id, $uri, $camera, $outroot, $dbname, $run_state, $reduction, $threads, $verbose,
      $no_update, $save_temps, $no_op, $redirect, $magicked, $deburned );
+
+my $zaplog = 0;
+
 GetOptions(
     'exp_id=s'          => \$exp_id,    # Exposure identifier
@@ -62,4 +65,5 @@
     'no-op'             => \$no_op,     # Don't do any operations?
     'redirect-output'   => \$redirect,
+    'zaplog'            => \$zaplog,
     'save-temps'        => \$save_temps, # Save temporary files?
     ) or pod2usage( 2 );
@@ -90,5 +94,5 @@
 my ($logDest, $traceDest);
 if ($run_state eq 'new') {
-    $logDest = prepare_output("LOG.IMFILE", $outroot, $class_id, 0);
+    $logDest = prepare_output("LOG.IMFILE", $outroot, $class_id, $zaplog);
     $traceDest = prepare_output("TRACE.IMFILE",  $outroot, $class_id, 1);
 } else {
Index: /trunk/ippScripts/scripts/diff_skycell.pl
===================================================================
--- /trunk/ippScripts/scripts/diff_skycell.pl	(revision 31940)
+++ /trunk/ippScripts/scripts/diff_skycell.pl	(revision 31941)
@@ -40,4 +40,6 @@
 my ($skycell_id, $diff_skyfile_id);
 my ($use_convolved);
+my $zaplog = 0;
+
 GetOptions(
     'diff_id=s'         => \$diff_id, # Diff identifier
@@ -55,4 +57,5 @@
     'no-op'             => \$no_op, # Don't do any operations?
     'redirect-output'   => \$redirect,
+    'zaplog'            => \$zaplog, # delete any previous log file
 ) or pod2usage( 2 );
 
@@ -82,4 +85,6 @@
     $logDest .= '.update';
     # ... well we can just do the dirty work here
+    $ipprc->kill_file($logDest);
+} elsif ($zaplog) {
     $ipprc->kill_file($logDest);
 }
Index: /trunk/ippScripts/scripts/warp_skycell.pl
===================================================================
--- /trunk/ippScripts/scripts/warp_skycell.pl	(revision 31940)
+++ /trunk/ippScripts/scripts/warp_skycell.pl	(revision 31941)
@@ -38,4 +38,6 @@
 
 my ($warp_id, $skycell_id, $warp_skyfile_id, $tess_dir, $reduction, $camera, $dbname, $outroot, $threads, $run_state, $magicked, $verbose, $no_update, $no_op, $redirect, $save_temps);
+my $zaplog = 0;
+
 GetOptions(
     'warp_id|i=s'         => \$warp_id, # Warp identifier
@@ -53,4 +55,5 @@
     'no-update'           => \$no_update, # Don't update the database?
     'no-op'               => \$no_op, # Don't do any operations?
+    'zaplog'              => \$zaplog, # delete previous logfile
     'redirect-output'     => \$redirect,
     'save-temps'          => \$save_temps, # Save temporary files?
@@ -74,5 +77,5 @@
 my $do_stats;
 if ($run_state eq 'new') {
-    $logDest = prepare_output("LOG.EXP", $outroot, $skycell_id, 0);
+    $logDest = prepare_output("LOG.EXP", $outroot, $skycell_id, $zaplog);
     $traceDest = prepare_output("TRACE.EXP", $outroot, $skycell_id, 1);
     $do_stats = 1;
Index: /trunk/tools/regenerateinput.pl
===================================================================
--- /trunk/tools/regenerateinput.pl	(revision 31941)
+++ /trunk/tools/regenerateinput.pl	(revision 31941)
@@ -0,0 +1,242 @@
+#!/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 $tooldir = "/home/panstarrs/bills/ipp/tools";
+my $dbname = "gpc1";
+my ($stage, $stage_id, $component, $threads, $update, $redirect, $pretend, $save_temps, $verbose);
+my $zaplog = 1;
+
+GetOptions(
+    'stage=s'           => \$stage,
+    'stage_id=i'        => \$stage_id,
+    'component=s'       => \$component,
+    'threads=i'         => \$threads,
+    'pretend'           => \$pretend,
+    'redirect-output'   => \$redirect,
+    'zaplog'            => \$zaplog,
+    'update'            => \$update,
+    'dbname=s'          => \$dbname,
+    'verbose'           => \$verbose, 
+    'save-temps'        => \$save_temps,
+) or pod2usage( 2 );
+
+pod2usage( -msg => "Unknown option: @ARGV", -exitval => 2 ) if @ARGV;
+pod2usage( -msg => "--stage and --stage_id are required", -exitval => 2 )
+    if !$stage or !$stage_id;
+pod2usage( -msg => "--component is required for $stage stage", -exitval => 2 ) if !$component and $stage ne 'camera';
+
+my $ipprc =  PS::IPP::Config->new();
+my $dbh = getDBHandle();
+
+$component = "" if !defined $component;
+
+my $camQuery = "SELECT fault, concat_ws('.', camProcessedExp.path_base, 'log') AS logfile 
+FROM camRun join camProcessedExp using(cam_id) WHERE cam_id = $stage_id";
+
+my $warpQuery = "SELECT fault, skycell_id, concat_ws('.', warpSkyfile.path_base, 'log') AS logfile 
+FROM warpRun join warpSkyfile using(warp_id) WHERE warp_id = $stage_id and skycell_id = '$component'";
+
+my $diffQuery = "SELECT fault, skycell_id, concat_ws('.', diffSkyfile.path_base, 'log') AS logfile 
+FROM diffRun join diffSkyfile using(diff_id) WHERE diff_id = $stage_id and skycell_id = '$component'";
+
+# list of error strings to look for
+my @camList  = ('Failed to convert file name ');
+my @warpList = ('Unable to find instance of Nebulous handle ');
+my @diffList = ('Unable to find instance of Nebulous handle ');
+
+my $query;
+my $list;
+if ($stage eq 'camera') {
+    $query = $camQuery;
+    $list = \@camList;
+} elsif ($stage eq 'warp') {
+    $query = $warpQuery;
+    $list = \@warpList;
+} elsif ($stage eq 'diff') {
+    $query = $diffQuery;
+    $list = \@diffList;
+} else {
+    die "unexpected stage: $stage";
+}
+
+# find the log file
+my $stmt = $dbh->prepare($query);
+$stmt->execute();
+my $results = $stmt->fetchrow_hashref();
+die "query returned no results\n" if !$results;
+
+my $logfile = $results->{logfile};
+die "log file name not found\n" if !$logfile;
+
+my $fault = $results->{fault};
+die "stage $stage_id $component not faulted\n" unless $fault;
+
+my $skycell_id = $results->{skycell_id};
+
+my $resolved = `neb-locate -p $logfile`;
+chomp $resolved;
+die "failed to locate log file for $stage $stage_id $component" if !$resolved;
+die "failed to access log file for $stage $stage_id $component" if ! -r $resolved;
+
+my $log = `tail -n 100 $resolved`;
+
+my @lines = split '\n', $log;
+my $match_line;
+my $badfile;
+foreach my $line (@lines) {
+    foreach my $str (@$list) {
+        if ($line =~ /$str/) {
+            print STDERR "found $str in $line\n" if $verbose;
+            $match_line = $line;
+
+            # fine the str in the line
+            my $n = index($line, $str);
+            # create a substring containing the text after $str
+            my $substr = substr $line, $n + length($str);
+            # The first word is the nebulous pathname for the bad file
+            ($badfile) = split " ", $substr;
+            $badfile =~ s/://;
+            last;
+        }
+    }
+    last if $match_line;
+}
+
+if (!$match_line or !$badfile) {
+    die "unable to resolve fault for $stage $stage_id $component\n";
+}
+print "Bad file is: $badfile\n" if $verbose;
+
+my $base = basename($badfile);
+print "base: $base\n" if $verbose;
+
+my $command;
+if ($stage eq 'camera') {
+    my ($exp_name, $exp_id, undef, $chip_id, $class_id) = split '\.', $base;
+    $command = "runchipimfile.pl --chip_id $chip_id --class_id $class_id --redirect-output";
+} elsif ($stage eq 'warp') {
+    if ($base =~ /\.ch\./) {
+        # problem is with a chip output
+        my ($exp_name, $exp_id, undef, $chip_id, $class_id) = split '\.', $base;
+        $command = "runchipimfile.pl --chip_id $chip_id --class_id $class_id --redirect-output";
+    } else {
+        die "don't know how to deal with bad $badfile yet\n";
+    }
+} elsif ($stage eq 'diff') {
+    if ($base =~ /\.wrp\./) {
+        # problem is with a warp output
+        my ($exp_name, $exp_id, undef, $warp_id) = split '\.', $base;
+        $command = "runwarpskycell.pl --warp_id $warp_id --skycell_id $skycell_id --redirect-output";
+    } else {
+        die "don't know how to deal with bad $badfile yet\n";
+    }
+} else {
+    die "not done with $stage yet\n";
+}
+
+
+$command .= " --zaplog" if $zaplog;
+
+if (!$pretend) {
+    my $rc = system "perl $tooldir/$command";
+    if ($rc) {
+        my $status = $rc >> 8;
+        die "$command failed with $rc $status";
+    }
+} else {
+    print "skipping: $command\n";
+}
+
+exit 0;
+
+
+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 $dbh;
+}
+
+__END__
+
+=pod
+
+=head1 NAME
+
+regenerateinput.pl - regenerate missing or damaged inputs for a component
+
+=head1 SYNOPSIS
+    
+    XXX: pod TODO
+
+    perl runwarpskyfile.pl --warp_id <warp_id> --skycell_id <skycell_id> [--threads <num_threads>] [--update] [--redirect-output] [--pretend] [--dbname <dbname>]
+
+Query the database for the results of a warp skycell and rerun the processing, optionally reverting a faulted
+run.
+
+=over 4
+
+=item * --warp_id <warp_id>
+
+The id of the warpSkyfile run to process.
+
+=item * --skycell_id <skycell_id>
+
+The skycell_id of the warpSkyfile run to process.
+
+=item * --threads <num_threads>
+
+The number of threads to use. Default 1.
+Optional.
+
+
+=item * --update
+
+Revert a faulted skycell before processing. If the skycell is not faulted no processing is done.
+WARNING: insure that the standard science procesing either has warp stage turned off or the
+label of this warpRun ommited from the list of labels otherwise it may attempt to processes this run at the same time.
+Optional.
+
+=item *  --redirect-output
+
+Send the output of the command to the logfile. (This is the default if --update is supplied).
+Optional.
+
+=item * --pretend
+
+Just print the commands that would be executed, but do not run them.
+Optional.
+
+=item * --dbname <dbname>
+
+Name of the IPP databse to query. Default is 'gpc1'.
+Optional.
+
+
+=head1 SEE ALSO
+L<runchipimfile.pl>, L<runcameraexp.pl>, L<rundiffskyfile.pl>
+
+=cut
Index: /trunk/tools/runchipimfile.pl
===================================================================
--- /trunk/tools/runchipimfile.pl	(revision 31940)
+++ /trunk/tools/runchipimfile.pl	(revision 31941)
@@ -18,4 +18,6 @@
 my ($chip_id, $class_id, $threads, $update, $redirect, $pretend, $save_temps);
 
+my $zaplog;
+
 GetOptions(
     'chip_id=i'         => \$chip_id,
@@ -23,4 +25,5 @@
     'threads=i'         => \$threads,
     'pretend'           => \$pretend,
+    'zaplog'            => \$zaplog,
     'redirect-output'   => \$redirect,
     'update'            => \$update,
@@ -95,8 +98,21 @@
     }
 }
-print "command to process this skycell\n";
+print "command to process this chip\n";
 print "$command\n";
 
 exit 0 if $pretend;
+
+# XXX: implement this in chip_imfile.pl
+if ($zaplog) {
+    my $logfile = $path_base . ".$class_id.log";
+    my $cmd = "neb-mv $logfile $logfile.trash";
+    print "$cmd\n";
+    my $rc = system $cmd;
+    if ($rc) {
+        my $status = $rc >> 8;
+        print STDERR "neb-mv failed with $rc $status\n";
+        exit $status;
+    }
+}
 
 exit system $command;
Index: /trunk/tools/rundiffskycell.pl
===================================================================
--- /trunk/tools/rundiffskycell.pl	(revision 31940)
+++ /trunk/tools/rundiffskycell.pl	(revision 31941)
@@ -26,4 +26,5 @@
 my $dbname = "gpc1";
 my ($diff_id, $skycell_id, $threads, $update, $redirect);
+my $zaplog;
 
 GetOptions(
@@ -32,4 +33,5 @@
     'threads=i'         => \$threads,
     'redirect-output'   => \$redirect,
+    'zaplog'            => \$zaplog,
     'update'            => \$update,
     'pretend'           => \$pretend,
@@ -74,4 +76,5 @@
 $command .= " --reduction $reduction" if $reduction;
 $command .= " --threads $threads" if $threads;
+$command .= " --zaplog" if $zaplog;
 
 print "command to process this skycell\n";
Index: /trunk/tools/runwarpskycell.pl
===================================================================
--- /trunk/tools/runwarpskycell.pl	(revision 31940)
+++ /trunk/tools/runwarpskycell.pl	(revision 31941)
@@ -17,4 +17,5 @@
 my $dbname = "gpc1";
 my ($warp_id, $skycell_id, $threads, $update, $redirect, $pretend, $save_temps);
+my $zaplog;
 
 GetOptions(
@@ -23,4 +24,5 @@
     'threads=i'         => \$threads,
     'pretend'           => \$pretend,
+    'zaplog'            => \$zaplog,
     'redirect-output'   => \$redirect,
     'update'            => \$update,
@@ -103,4 +105,18 @@
 exit 0 if $pretend;
 
+# XXX: implement this in warp_skycell.pl
+if ($zaplog) {
+    my $logfile = $path_base . ".log";
+    my $cmd = "neb-mv $logfile $logfile.trash";
+    print "$cmd\n";
+    my $rc = system $cmd;
+    if ($rc) {
+        my $status = $rc >> 8;
+        print STDERR "neb-mv failed with $rc $status\n";
+        exit $status;
+    }
+}
+
+
 exit system $command;