Index: /tags/ipp-pv3-20140717/ippScripts/scripts/sc_prepare_staticsky.pl
===================================================================
--- /tags/ipp-pv3-20140717/ippScripts/scripts/sc_prepare_staticsky.pl	(revision 37441)
+++ /tags/ipp-pv3-20140717/ippScripts/scripts/sc_prepare_staticsky.pl	(revision 37441)
@@ -0,0 +1,334 @@
+#! /usr/bin/env perl
+
+# generate the input & output files lists and commands for a single staticskyRun.
+
+use Carp;
+use warnings;
+use strict;
+
+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 DateTime;
+use Data::Dumper;
+use File::Basename;
+
+use Getopt::Long qw( GetOptions :config auto_help auto_version gnu_getopt );
+use Pod::Usage qw( pod2usage );
+
+# Hard coded values
+# my $remote_root   = '/lustre/scratch1/turquoise/watersc1/ps1/'; # Far side destination base location
+my $remote_root     = '/scratch3/watersc1/';  # Far side destination base location
+my $remote_hostname = "LANL/Mustang";         # Name of the remote node.
+my $threads_req     = 4;                      # How many threads are we going to use?
+
+my $fail_state = "prep_fail";
+
+# Look for programs we need
+my $missing_tools;
+my $remotetool = can_run('remotetool') or (warn "Can't find remotetool" and $missing_tools = 1);
+my $stacktool    = can_run('stacktool') or (warn "Can't find stacktool" and $missing_tools = 1);
+my $staticskytool= can_run('staticskytool') or (warn "Can't find staticskytool" and $missing_tools = 1);
+
+if ($missing_tools) {
+    warn("Can't find required tools.");
+    exit($PS_EXIT_CONFIG_ERROR);
+}
+
+my ($remote_id,$stack_id,$camera,$dbname,$verbose,$path_base,$no_update);
+GetOptions(
+    'remote_id=s'    => \$remote_id,
+    'sky_id=s'       => \$sky_id,
+    'camera|c=s'     => \$camera,
+    'dbname|d=s'     => \$dbname,
+    'path_base=s'    => \$path_base,
+    'no_update'      => \$no_update,
+    'verbose'        => \$verbose,
+    ) or pod2usage( 2 );
+
+pod2usage( -msg => "Unknown option: @ARGV", -exitval => 2 ) if @ARGV;
+pod2usage( -msg => "Required options: --remote_id --sky_id --camera --dbname --path_base", -exitval => 3) unless
+    defined($remote_id) and
+    defined($sky_id) and
+    defined($camera) and
+    defined($path_base) and
+    defined($dbname);
+
+my $ipprc = PS::IPP::Config->new( $camera ) or &my_die( "Unable to set up", $remote_id, $sky_id, $PS_EXIT_CONFIG_ERROR, $fail_state);
+
+my $mdcParser = PS::IPP::Metadata::Config->new; # Parser for metadata config files
+
+my @return_component_list = ("LOG.EXP", 
+			     "PSPHOT.CHISQ.IMAGE","PSPHOT.CHISQ.MASK","PSPHOT.CHISQ.VARIANCE");
+                             
+my @return_component_list_per_input = ("PSPHOT.STACK.OUTPUT.IMAGE","PSPHOT.STACK.OUTPUT.MASK","PSPHOT.STACK.OUTPUT.VARIANCE","PSPHOT.STACK.OUTPUT");
+
+# STEP 0: Open output files
+my $uri_transfer= $path_base . ".transfer";
+my $uri_check   = $path_base . ".check";
+my $uri_config  = $path_base . ".config";
+my $uri_generate= $path_base . ".generate";
+my $uri_return  = $path_base . ".return";
+
+my $disk_transfer= $ipprc->file_resolve($uri_transfer,1);
+my $disk_check   = $ipprc->file_resolve($uri_check,1);
+my $disk_config  = $ipprc->file_resolve($uri_config,1);
+my $disk_generate= $ipprc->file_resolve($uri_generate,1);
+my $disk_return  = $ipprc->file_resolve($uri_return,1);
+
+my (undef, $remote_config) = &uri_convert($uri_config); # Needs to be done after we've created it.
+
+open(TRANSFER, ">$disk_transfer")  || &my_die("Couldn't open file? $disk_transfer",$remote_id, $sky_id, $PS_EXIT_SYS_ERROR, $fail_state);
+open(CHECK,    ">$disk_check")     || &my_die("Couldn't open file? $disk_check",   $remote_id, $sky_id, $PS_EXIT_SYS_ERROR, $fail_state);
+open(CONFIG,   ">$disk_config")    || &my_die("Couldn't open file? $disk_config",  $remote_id, $sky_id, $PS_EXIT_SYS_ERROR, $fail_state);
+open(GENERATE, ">$disk_generate")  || &my_die("Couldn't open file? $disk_generate",$remote_id, $sky_id, $PS_EXIT_SYS_ERROR, $fail_state);
+open(RETURN,   ">$disk_return")    || &my_die("Couldn't open file? $disk_return",  $remote_id, $sky_id, $PS_EXIT_SYS_ERROR, $fail_state);
+
+my $job_index = 0;
+
+# STEP 1: Get exposure level information from the stackRun we're working from.
+my ($reduction, $workdir, $tess_id, $skycell_id);
+{
+    my $command = "$staticskytool -pendingskycalrun -sky_id $sky_id";
+    $command .= " -dbname $dbname " if defined($dbname);
+    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 run staticskytool -inputs ", $remote_id, $sky_id, $error_code, $fail_state);
+    }
+
+    my $MDlist = $mdcParser->parse(join "", @$stdout_buf) or
+        &my_die("Unable to determine stack component information.", $remote_id, $sky_id, $PS_EXIT_PROG_ERROR, $fail_state);
+    my $metadata = parse_md_list($MDlist);
+
+    my $stack = $metadata->[0];
+
+    $reduction = $stack->{reduction};
+    $reduction = 'DEFAULT' unless defined($reduction);
+    $workdir   = $stack->{workdir};
+    $tess_id   = $stack->{tess_id};
+    $skycell_id= $stack->{skycell_id};
+}
+my $ipp_outroot    = "${workdir}/${tess_id}/${skycell_id}/${tess_id}.${skycell_id}.sky.${sky_id}";
+my $remote_outroot = &uri_local_to_remote($ipp_outroot);
+my $remote_outdir  = &uri_local_to_remote("${workdir}/${tess_id}/${skycell_id}");
+
+# STEP 2: Get the list of inputs
+my ($inputData);
+{
+    # This actually returns all the individual stack/skyfiles that comprise this run.  Because consistency.
+    my $command = "$staticskytool -inputs -sky_id $sky_id ";
+    $command .= " -dbname $dbname " if defined($dbname);
+    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 run stacktool -inputskyfile ", $remote_id, $sky_id, $error_code, $fail_state);
+    }
+
+    my $MDlist = $mdcParser->parse(join "", @$stdout_buf) or
+        &my_die("Unable to determine stack component information.", $remote_id, $sky_id, $PS_EXIT_PROG_ERROR, $fail_state);
+    $inputData = parse_md_list($MDlist);
+}
+
+# STEP 3: Iterate over the sub-components
+{
+    # Generate a file mapping the symbolic and "disk" representations of each needed file.
+    my $uri_compmap   = "${ipp_outroot}.compmap";
+    my $component_map = $ipprc->file_resolve($uri_compmap,1);    
+    my ($ipp_compmap, $remote_compmap) = &uri_to_outputs($component_map);
+    open(COMPMAP,">$ipp_compmap") || &my_die("Couldn't open file? $ipp_compmap",  $remote_id, $sky_id, $PS_EXIT_SYS_ERROR, $fail_state);
+    
+    # Loop over all needed components for this stack.
+    my $nInputs = 0;
+    my $input_path_base_string = "";
+    foreach my $inputEntry ( @{ $inputData } ) {
+	my $input_stack_id  = $inputEntry->{stack_id};
+
+        my $input_path_base = $inputEntry->{path_base};
+        my $remote_path_base = &uri_local_to_remote($input_path_base);
+        $input_path_base_string .= " $remote_path_base ";
+	$input_path_base_string .= " $stack_id ";
+        if ($verbose) { print STDERR "$input_path_base_string\n"; }
+
+        # Append file names to transfer lists so we can recover if inputs are deleted.
+	my $remote_file;
+	my $ipp_disk;
+	#  ${remote_root}/tmp/${ipp_disk}
+        (undef,$remote_file) = &uri_to_outputs($input_path_base . ".unconv.fits");
+	($ipp_disk,undef)    = &uri_convert($input_path_base . ".unconv.fits");
+	print COMPMAP "$remote_file ${remote_root}/tmp/${ipp_disk}\n";
+        (undef,$remote_file) = &uri_to_outputs($input_path_base . ".unconv.wt.fits");
+	($ipp_disk,undef)    = &uri_convert($input_path_base . ".unconv.wt.fits");
+	print COMPMAP "$remote_file ${remote_root}/tmp/${ipp_disk}\n";
+        (undef,$remote_file) = &uri_to_outputs($input_path_base . ".unconv.mask.fits");
+	($ipp_disk,undef)    = &uri_convert($input_path_base . ".unconv.mask.fits");
+	print COMPMAP "$remote_file ${remote_root}/tmp/${ipp_disk}\n";
+        (undef,$remote_file) = &uri_to_outputs($input_path_base . ".unconv.num.fits");
+	($ipp_disk,undef)    = &uri_convert($input_path_base . ".unconv.num.fits");
+	print COMPMAP "$remote_file ${remote_root}/tmp/${ipp_disk}\n";
+        (undef,$remote_file) = &uri_to_outputs($input_path_base . ".cmf");
+	($ipp_disk,undef)    = &uri_convert($input_path_base . ".cmf");
+	print COMPMAP "$remote_file ${remote_root}/tmp/${ipp_disk}\n";
+	(undef,$remote_file) = &uri_to_outputs($input_path_base . ".psf");
+	($ipp_disk,undef)    = &uri_convert($input_path_base . ".psf");
+	print COMPMAP "$remote_file ${remote_root}/tmp/${ipp_disk}\n";
+
+	$nInputs++;
+    }
+
+    close(COMPMAP);
+
+    my $mk_mdc_command = "mkdir -p $remote_outdir && sc_mk_staticsky_mdc.pl --compmap ${remote_root}/tmp/${component_map} $input_path_base_string > ${remote_outroot}.in.mdc";
+    my $recipe_psphot = $ipprc->reduction($reduction, 'STACKPHOT_PSPHOT');
+    my $recipe_ppsub  = $ipprc->reduction($reduction, 'STACKPHOT_PPSUB');
+    my $recipe_ppstack= $ipprc->reduction($reduction, 'STACKPHOT_PPSTACK'); # Recipe to use
+
+    my $pps_command  = " psphotStack -input ${remote_outroot}.in.mdc ";
+    $pps_command    .= " ${remote_outroot} -stats ${remote_outroot}.stats ";
+    $pps_command    .= " -recipe PSPHOT $recipe_psphot ";
+    $pps_command    .= " -recipe PPSUB  $recipe_ppsub ";
+    $pps_command    .= " -recipe PPSTACK $recipe_ppstack ";
+    $pps_command    .= " -tracedest ${remote_outroot}.trace -log ${remote_outroot}.log ";
+    $pps_command    .= " -threads $threads_req ";
+    $pps_command    .= " -dumpconfig ${remote_outroot}.mdc ";
+
+    my $post_cmd_echo = " echo -n \"staticskytool  -addresult -sky_id $sky_id ";
+    $post_cmd_echo   .= " -path_base $ipp_outroot -uri UNKNOWN -num_inputs $nInputs ";
+    $post_cmd_echo   .=  " -dbname $dbname " if defined $dbname;
+    $post_cmd_echo   .= " -hostname $remote_hostname -dtime_script 0 \" > ${remote_outroot}.dbinfo ";
+
+# CZW: 2014-09-26 We currently do not save any information into the database here, so I'm leaving the dummy from stack.
+#    my $post_cmd_SfM  = " ppStatsFromMetadata ${remote_outroot}.stats - STACK_SKYCELL >> ${remote_outroot}.dbinfo ";
+#    print CONFIG "${mk_mdc_command} && ${pps_command} && ${post_cmd_echo} && ${post_cmd_SfM} ";
+
+    print CONFIG "${mk_mdc_command} && ${pps_command} && ${post_cmd_echo} ";
+    $job_index++;
+
+    # Determine which output files need to be returned
+    foreach my $component(@return_component_list) {
+        my $filename = $ipprc->filename($component,$ipp_outroot);
+        my ($ipp_disk, $remote_disk) = &uri_to_outputs_for_return( $filename);
+        my $remote_outroot_dir = dirname($ipp_disk);
+        print CONFIG " && mkdir -p ${remote_root}/tmp/${remote_outroot_dir} && ln -sf $remote_disk ${remote_root}/tmp/${ipp_disk} && touch $remote_disk ";
+    }
+    # But this creates outputs for each input stack, so iterate over those as well.
+    foreach my $inputEntry (@{ $inputData }) {
+	my $stack_id = $inputEntry->{stack_id};
+	foreach my $component (@return_component_list_per_input) {
+	    my $filename = $ipprc->filename($component,$ipp_outroot,$stack_id);
+	    my ($ipp_disk, $remote_disk) = &uri_to_outputs_for_retrun( $filename );
+	    my $remote_outroot_dir = dirname($ipp_disk);
+	    print CONFIG " && mkdir -p ${remote_root}/tmp/${remote_outroot_dir} && ln -sf $remote_disk ${remote_root}/tmp/${ipp_disk} && touch $remote_disk ";
+	}
+    }
+	
+    print CONFIG "\n";
+}
+close(CONFIG);
+close(TRANSFER);
+close(CHECK);
+close(RETURN);
+close(GENERATE);
+
+unless($no_update) {
+    my $command = "remotetool -updatecomponent -remote_id $remote_id -stage_id $sky_id ";
+    $command .= " -set_jobs $job_index";
+    $command .= " -set_path_base $path_base";
+    $command .= " -set_state prep_done";
+    $command .= " -dbname $dbname " if defined $dbname;
+
+    system($command);
+}
+
+## Common SC routines
+
+# KEEP
+sub uri_convert { # (ipp_disk,remote_disk) = uri_convert(neb_uri);
+    my $neb_uri = shift;
+    my $ipp_disk= $ipprc->file_resolve( $neb_uri );
+    my $remote_disk = $ipp_disk;
+
+    unless(defined($ipp_disk)) {
+        &my_die( "Unable to generate file for $neb_uri ", $remote_id, $sky_id, $PS_EXIT_SYS_ERROR, $fail_state);
+    }
+
+    $remote_disk =~ s%^.*/%%;   # Remove nebulous path
+    $remote_disk =~ s%^\d+\.%%; # Remove ins_id
+    $remote_disk =~ s%:%/%g;    # Replace colons with directories
+    $remote_disk = "${remote_root}/${remote_disk}";
+    return($ipp_disk,$remote_disk);
+}
+
+# KEEP
+sub uri_convert_and_create { # (ipp_disk,remote_disk) = uri_convert_and_create(neb_uri); ipp_disk is created if it doesn't exist
+    my $neb_uri = shift;
+    my $ipp_disk= $ipprc->file_resolve( $neb_uri , 1);
+    my $remote_disk = $ipp_disk;
+
+    unless(defined($ipp_disk)) {
+        &my_die( "Unable to generate file for $neb_uri ", $remote_id, $sky_id, $PS_EXIT_SYS_ERROR, $fail_state);
+    }
+
+    $remote_disk =~ s%^.*/%%;   # Remove nebulous path
+    $remote_disk =~ s%^\d+\.%%; # Remove ins_id
+    $remote_disk =~ s%:%/%g;    # Replace colons with directories
+    $remote_disk = "${remote_root}/${remote_disk}";
+    return($ipp_disk,$remote_disk);
+}
+
+# KEEP
+sub uri_to_outputs { # (ipp_disk,remote_disk) = uri_to_output(neb_uri); Appends to TRANSFER and CHECK filehandles
+    my $neb_uri = shift;
+    my ($ipp_disk, $remote_disk) = uri_convert( $neb_uri );
+
+    print TRANSFER "$ipp_disk\n";
+    print CHECK    "$remote_disk\n";
+    return($ipp_disk,$remote_disk);
+}
+
+# KEEP
+sub uri_to_outputs_for_return { # (ipp_disk,remote_disk) = uri_to_outputs_for_return(neb_uri); create ipp_disk, append to RETURN and GENERATE
+    my $neb_uri = shift;
+    my ($ipp_disk, $remote_disk) = uri_convert_and_create( $neb_uri );
+
+    print RETURN "$ipp_disk\n";
+    print GENERATE "$remote_disk\n";
+    return($ipp_disk,$remote_disk);
+}
+
+# KEEP
+sub uri_local_to_remote { #(remote_uri) = uri_local_to_remote(local_neb_uri);
+    # This needs to replace the nebulous tag with the remote root.
+    my $local_uri = shift;
+    $local_uri =~ s%^.*?/%%; # neb:/
+    $local_uri =~ s%^.*?/%%; # /
+    $local_uri =~ s%^.*?/%%; # @HOST@.0/
+    my $remote_uri = "${remote_root}/" . $local_uri;
+
+    return($remote_uri);
+}
+
+sub my_die { # exit with status; my_die(message,stage_id,exit_code,exit_status);
+    my $msg = shift;
+    my $remote_id  = shift;
+    my $stage_id  = shift;
+    my $exit_code = shift;
+    my $exit_state = shift;
+
+    $exit_code = $PS_EXIT_PROG_ERROR unless defined $exit_code;
+
+    carp($msg);
+
+    if (defined $remote_id and defined $stage_id and not $no_update) {
+        my $command = "remotetool -updatecomponent -remote_id $remote_id -stage_id $stage_id";
+        $command .= " -set_state $exit_state " if defined $exit_state;
+        $command .= " -dbname $dbname " if defined $dbname;
+
+        system($command);
+    }
+
+    exit($exit_code);
+}