Index: /trunk/ippScripts/scripts/dist_fix_file.pl
===================================================================
--- /trunk/ippScripts/scripts/dist_fix_file.pl	(revision 32948)
+++ /trunk/ippScripts/scripts/dist_fix_file.pl	(revision 32948)
@@ -0,0 +1,234 @@
+#!/usr/bin/env perl
+
+use Carp;
+use warnings;
+use strict;
+
+## report the program and machine
+use Sys::Hostname;
+my $host = hostname();
+my $date = `date`;
+#print "\n\n";
+#print "Starting script $0 on $host at $date\n\n";
+
+use vars qw( $VERSION );
+$VERSION = '0.01';
+
+use IPC::Cmd 0.36 qw( can_run run );
+use File::Temp qw( tempfile );
+use File::Basename qw( basename );
+use Digest::MD5::File qw( file_md5_hex );
+use PS::IPP::Metadata::Config;
+use PS::IPP::Metadata::List qw( parse_md_list );
+use PS::IPP::Config 1.01 qw( :standard );
+
+use DBI;
+
+use Getopt::Long qw( GetOptions :config auto_help auto_version gnu_getopt );
+use Pod::Usage qw( pod2usage );
+
+# Look for programs we need
+my $missing_tools;
+my $disttool   = can_run('disttool') or (warn "Can't find disttool" and $missing_tools = 1);
+my $regtool   = can_run('regtool') or (warn "Can't find regtool" and $missing_tools = 1);
+my $dist_component   = can_run('dist_component.pl') or (warn "Can't find dist_component.pl" and $missing_tools = 1);
+if ($missing_tools) {
+    warn("Can't find required tools.");
+    exit($PS_EXIT_CONFIG_ERROR);
+}
+
+# Parse the command-line arguments
+my ($dist_id, $camera, $component );
+my ($outdir, $run_state, $data_state, $magicked, $poor_quality, $exp_type, $rerun);
+my ($dbname, $save_temps, $verbose, $no_update, $logfile);
+
+$camera = 'GPC1';
+
+GetOptions(
+           'dist_id=s'      => \$dist_id,    # distribution run identifier
+           'component=s'    => \$component,  # the class_id or skycell_id
+           'camera=s'       => \$camera,     # the class_id or skycell_id
+           'save-temps'     => \$save_temps, # Save temporary files?
+           'dbname=s'       => \$dbname,     # Database name
+           'verbose'        => \$verbose,    # Print stuff?
+           'no-update'      => \$no_update,  # Don't update the database?
+           'logfile=s'      => \$logfile,
+           ) or pod2usage( 2 );
+
+pod2usage( -msg => "Unknown option: @ARGV", -exitval => 2 ) if @ARGV;
+pod2usage( -msg => "Required options: --dist_id --camera --component",
+           -exitval => 3) unless
+    defined $dist_id and
+    defined $camera and
+    defined $component;
+
+my $ipprc = PS::IPP::Config->new($camera); # IPP configuration
+$ipprc->redirect_to_logfile($logfile) if $logfile;
+
+my $dbh = getDBHandle() unless $no_update;
+
+my $temproot = metadataLookupStr($ipprc->{_siteConfig}, "TEMP.DIR");
+
+$temproot = "/tmp" if !defined $temproot;
+
+my $mdcParser = PS::IPP::Metadata::Config->new; # Parser for metadata config files
+
+$disttool .= " -dbname $dbname" if $dbname;
+$regtool .= " -dbname $dbname" if $dbname;
+
+my $comp = get_distcomponent($dist_id, $component);
+
+my $stage = $comp->{stage};
+my $stage_id = $comp->{stage_id};
+my $no_magic = $comp->{no_magic};
+my $path_base;
+my $stage_args = "";
+if ($stage eq 'raw') {
+    # need path_base (get from uri) 
+    # exp_type
+    # no_magic
+    # camera path base if !$no_magic
+    my $command = "$regtool -processedimfile -exp_id $stage_id -class_id $component";
+    my ( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) =
+        run(command => $command, verbose => $verbose);
+    unless ($success) {
+        $error_code = (($error_code >> 8) or $PS_EXIT_PROG_ERROR);
+        &my_die("Unable to perform $command: $error_code", $dist_id, $component, $outdir, $error_code);
+    }
+
+    my $metadata = $mdcParser->parse (join "", @$stdout_buf) or
+        &my_die("Unable to parse metadata config doc", $dist_id, $component, $outdir, $PS_EXIT_PROG_ERROR);
+
+    my $results = parse_md_list($metadata);
+
+    if ((scalar @$results) != 1) {
+        my $n = scalar @$results;
+        &my_die("Unexected number of results from regtool -processedimfile: $n", $dist_id, $component, $outdir, $PS_EXIT_PROG_ERROR);
+    }
+    my $rawfile = $results->[0];
+    $path_base = $rawfile->{uri};
+    $path_base =~ s/.fits//;
+    my $exp_type = $rawfile->{exp_type};
+    if (!$no_magic) {
+        die "don't know how to create magicked raw bundles yet\n";
+    }
+    $stage_args .= " --exp_type $exp_type --chip_path_base NULL";
+    $stage_args .= " --no_magic" if $no_magic;
+} else {
+
+    die "not ready for stage $stage yet\n";
+}
+my $dist_cmd = "$dist_component --rerun --camera $camera --dist_id $dist_id --stage $stage --stage_id $stage_id --component $component --outdir $comp->{outdir} --path_base $path_base $stage_args";
+
+$dist_cmd .= " --dbname $dbname" if $dbname;
+$dist_cmd .= " --verbose" if $verbose;
+$dist_cmd .= " --no-update" if $no_update;
+
+print "$dist_cmd\n";
+
+$comp = get_distcomponent($dist_id, $component);
+
+my $bytes = $comp->{bytes};
+my $md5sum = $comp->{md5sum};
+my $name = $comp->{name};
+
+
+my $query = "UPDATE dsFile join dsFileset using(fileset_id) join dsProduct USING(prod_id) SET dsFile.bytes =?, dsFile.md5sum = ? WHERE prod_name = ? AND fileset_name = ? AND file_name = ?";
+
+my $stmt = $dbh->prepare($query);
+
+my $filesets = get_filesets($dist_id);
+
+foreach my $fs (@$filesets) {
+    my $product = $fs->{product};
+    my $fileset = $fs->{fileset};
+    $stmt->execute($bytes, $md5sum, $product, $fileset, $name)  or
+        &my_die("failed to update dsFile for $product $fileset $name\n", $dist_id, $component, $outdir, $PS_EXIT_PROG_ERROR);
+
+    print "Updated dsFile for $product $fileset $name $bytes $md5sum\n";
+}
+
+
+exit 0;
+
+sub getDBHandle {
+    my $dbserver = metadataLookupStr($ipprc->{_siteConfig}, "DS_DBSERVER");
+    my $dbuser = metadataLookupStr($ipprc->{_siteConfig}, "DS_DBUSER");
+    my $dbpassword = metadataLookupStr($ipprc->{_siteConfig}, "DS_DBPASSWORD");
+    my $dbname = metadataLookupStr($ipprc->{_siteConfig}, "DS_DBNAME");
+
+    &my_die("database configuration not set up", $dist_id, $component, $outdir, $PS_EXIT_UNKNOWN_ERROR) unless defined($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 $dbname on $dbserver.\n";
+
+    return $dbh;
+}
+
+
+
+sub get_distcomponent {
+    my $dist_id = shift;
+    my $component = shift;
+    my $command = "$disttool -processedcomponent -dist_id $dist_id -component $component";
+    my ( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) =
+        run(command => $command, verbose => $verbose);
+    unless ($success) {
+        $error_code = (($error_code >> 8) or $PS_EXIT_PROG_ERROR);
+        &my_die("Unable to perform $command: $error_code", $dist_id, $component, $outdir, $error_code);
+    }
+
+    my $metadata = $mdcParser->parse (join "", @$stdout_buf) or
+        &my_die("Unable to parse metadata config doc", $dist_id, $component, $outdir, $PS_EXIT_PROG_ERROR);
+
+    my $results = parse_md_list($metadata);
+
+    if ((scalar @$results) != 1) {
+        my $n = scalar @$results;
+        &my_die("Unexected number of results from disttool -processedcomponent: $n", $dist_id, $component, $outdir, $PS_EXIT_PROG_ERROR);
+    }
+    return $results->[0];
+}
+
+sub get_filesets {
+    my $dist_id = shift;
+    my $command = "$disttool -listfilesets -dist_id $dist_id";
+    my ( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) =
+        run(command => $command, verbose => $verbose);
+    unless ($success) {
+        $error_code = (($error_code >> 8) or $PS_EXIT_PROG_ERROR);
+        &my_die("Unable to perform $command: $error_code", $dist_id, $component, $outdir, $error_code);
+    }
+
+    my $output = join "", @$stdout_buf;
+    if (!$output) {
+        return undef;
+    }
+    my $metadata = $mdcParser->parse ($output) or
+        &my_die("Unable to parse metadata config doc", $dist_id, $component, $outdir, $PS_EXIT_PROG_ERROR);
+
+    my $results = parse_md_list($metadata);
+
+    return $results
+}
+
+
+### Pau.
+sub my_die
+{
+    my $msg = shift;            # Warning message on die
+    my $dist_id = shift;        # distRun.dist_id
+    my $component = shift;      # class_id, skycell_id, or exposure
+    my $outdir = shift;         # output directory
+    my $exit_code = shift;      # Exit code to add
+
+    $exit_code = $PS_EXIT_PROG_ERROR unless defined $exit_code;
+
+    carp($msg);
+    exit $exit_code;
+}
+
+__END__