Index: trunk/ippScripts/scripts/publish_file.pl
===================================================================
--- trunk/ippScripts/scripts/publish_file.pl	(revision 24512)
+++ trunk/ippScripts/scripts/publish_file.pl	(revision 24512)
@@ -0,0 +1,198 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+## report the program and machine
+use Sys::Hostname;
+my $host = hostname();
+print "Starting script $0 on $host\n\n";
+
+use DateTime;
+my $mjd_start = DateTime->now->mjd;   # MJD of starting script
+
+use vars qw( $VERSION );
+$VERSION = '0.01';
+
+use IPC::Cmd 0.36 qw( can_run run );
+use PS::IPP::Metadata::Config;
+use PS::IPP::Metadata::List qw( parse_md_list );
+use PS::IPP::Config 1.01 qw( :standard );
+use File::Temp qw( tempfile );
+use File::Basename qw( basename );
+use Carp;
+
+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 $pubtool = can_run('pubtool') or (warn "Can't find pubtool" and $missing_tools = 1);
+my $camtool = can_run('camtool') or (warn "Can't find camtool" and $missing_tools = 1);
+my $difftool = can_run('difftool') or (warn "Can't find difftool" and $missing_tools = 1);
+my $ppMops = can_run('ppMops') or (warn "Can't find ppMops" and $missing_tools = 1);
+my $dsreg = can_run('dsreg') or (warn "Can't find dsreg" and $missing_tools = 1);
+if ($missing_tools) {
+    warn("Can't find required tools.");
+    exit($PS_EXIT_CONFIG_ERROR);
+}
+
+# Parse the command-line arguments
+my ( $pub_id, $camera, $stage, $stage_id, $format, $product, $workdir );
+my ( $dbname, $verbose, $no_update, $save_temps, $redirect );
+
+GetOptions(
+    'pub_id=s'          => \$pub_id, # Publish identifier
+    'camera=s'          => \$camera, # Camera name
+    'stage=s'           => \$stage,       # Stage of interest
+    'stage_id=s'        => \$stage_id,    # Stage identifier
+    'product=s'         => \$product,     # Datastore product name
+    'workdir=s'         => \$workdir,     # Working directory
+    'dbname=s'          => \$dbname,    # Database name
+    'verbose'           => \$verbose,   # Print to stdout
+    'no-update'         => \$no_update, # Don't update the database?
+    'save-temps'        => \$save_temps, # Save temporary files?
+    'redirect-output'   => \$redirect,   # Redirect output to log file?
+    ) or pod2usage( 2 );
+
+pod2usage( -msg => "Unknown option: @ARGV", -exitval => 2 ) if @ARGV;
+pod2usage( -msg => "Required options: --pub_id --camera --stage --stage_id --product --workdir",
+           -exitval => $PS_EXIT_CONFIG_ERROR) unless
+    defined $pub_id and
+    defined $camera and
+    defined $product and
+    defined $stage and
+    defined $stage_id and
+    defined $workdir;
+
+my $outroot = "$workdir/$product.$pub_id"; # Output root name
+
+my $ipprc = PS::IPP::Config->new( $camera ) or
+    &my_die( "Unable to set up", $pub_id, $PS_EXIT_CONFIG_ERROR ); # IPP configuration
+
+$ipprc->outroot_prepare( $outroot );
+my $logDest = "$outroot.log";
+$ipprc->redirect_output($logDest) or &my_die( "Unable to redirect output", $pub_id, $PS_EXIT_SYS_ERROR ) if $redirect;
+
+my $mdcParser = PS::IPP::Metadata::Config->new;
+
+
+# Retrieve file name of interest
+my %files;                      # Input filenames
+my %zp;                         # Zero points
+{
+    my $command;                # Command to run
+
+    if ($stage eq 'diff') {
+        $command =  "difftool -diffskyfile -diff_id $stage_id";
+    } elsif ($stage eq 'camera') {
+        $command =  "camtool -processedexp -cam_id $stage_id";
+    } else {
+        &my_die( "Unrecognised stage: $stage", $pub_id, $PS_EXIT_CONFIG_ERROR );
+    }
+    $command .= " -dbname $dbname" if defined $dbname;
+
+    my ( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) =
+        run(command => $command, verbose => $verbose);
+    &my_die( "Unable to retrieve filename", $pub_id, $PS_EXIT_SYS_ERROR) unless $success;
+
+    my $metadata = $mdcParser->parse(join "", @$stdout_buf) or
+        &my_die("Unable to parse metadata config", $pub_id, $PS_EXIT_PROG_ERROR);
+
+    my $components = parse_md_list($metadata) or
+        &my_die("Unable to parse metadata list", $pub_id, $PS_EXIT_PROG_ERROR);
+
+    foreach my $comp ( @$components ) {
+        my $path_base = $comp->{path_base}; # Base name for file
+        next if defined $comp->{quality} and $comp->{quality} > 0;
+
+        (carp "Bad zpt_obs or exp_time for component" and next) if not defined $comp->{zpt_obs} or not defined $comp->{exp_time};
+        my $zp = $comp->{zpt_obs} + 2.5 * log($comp->{exp_time}) / log(10);
+
+        if ($stage eq 'diff') {
+            my $skycell_id = $comp->{skycell_id};
+            $files{"$skycell_id.pos"} = $ipprc->filename( "PPSUB.OUTPUT.SOURCES", $path_base );
+            $files{"$skycell_id.neg"} = $ipprc->filename( "PPSUB.INVERSE.SOURCES", $path_base ) if
+                defined $comp->{bothways} and $comp->{bothways};
+            $zp{"$skycell_id.pos"} = $zp;
+            $zp{"$skycell_id.neg"} = $zp if defined $comp->{bothways} and $comp->{bothways};
+        } elsif ($stage eq 'camera') {
+            my $cam_id = $comp->{cam_id};
+            $files{$cam_id} = $ipprc->filename( "PSASTRO.OUTPUT", $path_base );
+            $zp{$cam_id} = $zp;
+        }
+    }
+}
+
+# Prepare for data store input
+my ($listFile, $listFileName) = tempfile("/tmp/publish.$pub_id.list.XXXX", UNLINK => !$save_temps );
+
+# Process each file
+foreach my $comp ( keys %files ) {
+    my $file = $ipprc->file_resolve( $files{$comp} ) or
+        &my_die("Unable to resolve file $files{$comp}", $pub_id, $PS_EXIT_SYS_ERROR);
+    my_die("Unable to find file $file", $pub_id, $PS_EXIT_PROG_ERROR) unless $ipprc->file_exists( $file );
+
+    my $zp = $zp{$comp};
+    if ($product eq "IPP-MOPS") {
+        my $out = $ipprc->file_resolve( "$outroot.$comp.fits" );
+        my $command = "$ppMops $file $zp $out";
+        my ( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) =
+            run(command => $command, verbose => $verbose);
+        &my_die( "Unable to translate $file", $pub_id, $PS_EXIT_SYS_ERROR) unless $success;
+        &my_die( "Unable to find translated file $out", $pub_id, $PS_EXIT_SYS_ERROR) unless $ipprc->file_exists( $out );
+        $file = $out;
+    }
+
+    # format: filename|filesize|md5sum|filetype|
+    # note: since we omit filesize and md5sum, dsreg will calculate them
+    print $listFile "$file|||$product|$comp|\n";
+}
+
+
+unless ($no_update) {
+    my $command = "$dsreg --add $stage.$stage_id --copy --abspath --product $product --type $product --list $listFileName";
+
+    my ( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) =
+        run(command => $command, verbose => $verbose);
+    &my_die( "Unable to register with data store", $pub_id, $PS_EXIT_SYS_ERROR) unless $success;
+}
+
+unless ($no_update) {
+    my $command = "$pubtool -add -pub_id $pub_id -path_base $outroot";
+    $command .= " -dbname $dbname" if defined $dbname;
+
+    my ( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) =
+        run(command => $command, verbose => $verbose);
+    &my_die( "Unable to register with data store", $pub_id, $PS_EXIT_SYS_ERROR) unless $success;
+}
+
+
+
+### Pau.
+
+
+sub my_die
+{
+    my $msg = shift;            # Exit message
+    my $pub_id = shift;         # Publish run identifier
+    my $fault = shift;          # Fault code
+
+    $fault = $PS_EXIT_PROG_ERROR unless defined $fault;
+
+    carp($msg);
+    if (defined $pub_id and not $no_update) {
+        my $command = "$pubtool -add";
+        $command .= " -pub_id $pub_id";
+        $command .= " -path_base $outroot";
+        $command .= " -fault $fault";
+        $command .= " -dbname $dbname" if defined $dbname;
+
+        my ( $success, $error_code, $full_buf, $stdout_buf, $stderr_buf ) =
+            run(command => $command, verbose => $verbose);
+    }
+    exit $fault;
+}
+
+
+__END__