Index: trunk/tools/test_destreak
===================================================================
--- trunk/tools/test_destreak	(revision 27408)
+++ trunk/tools/test_destreak	(revision 27408)
@@ -0,0 +1,219 @@
+#!/bin/env perl
+
+# given a run id or exposure find the various inputs and run
+# streaksremove 
+# Does not update the database or 'replace' the inputs
+
+use strict;
+use warnings;
+
+use Getopt::Long qw( GetOptions :config auto_help auto_version gnu_getopt );
+use Pod::Usage qw( pod2usage );
+use File::Temp qw( tempfile );
+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 qw( :standard );
+use File::Basename qw( basename dirname );
+
+
+my ($exp_id, $chip_id, $cam_id, $warp_id, $diff_id, $stage, $component);
+my ($outroot, $logfile, $dbname, $verbose, $save_temps);
+
+GetOptions(
+    'exp_id=s'      =>  \$exp_id,
+    'chip_id=s'     =>  \$chip_id,
+    'cam_id=s'      =>  \$cam_id,
+    'warp_id=s'     =>  \$warp_id,
+    'diff_id=s'     =>  \$diff_id,
+    'stage=s'       =>  \$stage,
+    'component=s'   =>  \$component,
+    'outroot=s'     =>  \$outroot,
+    'logfile=s'     =>  \$logfile,
+    'dbname'       =>   \$dbname,
+    'verbose'       =>  \$verbose,
+    'save-temps'    =>  \$save_temps,
+
+);
+
+pod2usage( -msg => "Unknown option: @ARGV", -exitval => 2 ) if @ARGV;
+pod2usage( -msg => "Required options: --chip_id | --cam_id | --warp_id | --diff_id --outroot",
+           -exitval => 3) unless
+    defined $outroot and
+    ((defined $exp_id and defined $stage) or
+     defined $chip_id or defined $cam_id or defined $warp_id or defined $diff_id);
+
+my $ipprc =  PS::IPP::Config->new();
+my $dbh = getDBHandle();
+
+my $camera = "GPC1";
+my $destreak_command = "magic_destreak.pl --camera $camera --outroot  $outroot";
+$destreak_command .= " --dbname $dbname" if $dbname;
+$destreak_command .= " --verbose" if $verbose;
+$destreak_command .= " --save-temps" if $save_temps;
+$destreak_command .= " --logfile $logfile" if $logfile;
+
+my $stmt;
+my $query;
+if ($chip_id) {
+    $stage = "chip";
+
+    $query =
+"SELECT
+    exp_id,
+    chip_id,
+    chipProcessedImfile.class_id,
+    chipProcessedImfile.magicked,
+    chipProcessedImfile.data_state,
+    magicDSRun.magic_ds_id,
+    magicMask.uri AS streaks_uri,
+    chipProcessedImfile.path_base,
+    magicDSFile.backup_path_base,
+    camProcessedExp.path_base AS cam_path_base
+    FROM chipRun 
+    JOIN chipProcessedImfile using(chip_id, exp_id)
+    JOIN camRun using(chip_id)
+    JOIN camProcessedExp using(cam_id)
+    JOIN magicDSRun ON stage = 'chip' AND stage_id = chipRun.chip_id 
+--  AND camRun.cam_id = magicDSRun.cam_id
+    JOIN magicDSFile ON magicDSRun.magic_ds_id = magicDSFile.magic_ds_id
+    AND class_id = component
+    JOIN magicRun using(magic_id, exp_id)
+    JOIN magicMask using(magic_id)
+    WHERE chipProcessedImfile.quality = 0
+        AND chipProcessedImfile.data_state = 'full'
+        AND chip_id = $chip_id";
+
+    $query .= " AND class_id = '$component'" if $component;
+    $stmt = $dbh->prepare($query);
+    $stmt->execute();
+
+    $destreak_command .= " --stage chip ";
+    my $processed = 0;
+    while (my $imfile = $stmt->fetchrow_hashref()) {
+        $processed++;
+        my $class_id = $imfile->{class_id};
+        my $path_base = $imfile->{path_base};
+        my $magicked = $imfile->{magicked};
+        my $streaks = $imfile->{streaks_uri};
+        my $cam_path_base = $imfile->{cam_path_base};
+        my $uri;
+        if ($magicked > 0) {
+            # get source of image from "backup"
+#            my $dirname = dirname($path_base);
+#            my $base = basename($path_base);
+#            $path_base = $dirname . "/SR_" . $base;
+            $path_base = $imfile->{backup_path_base};
+        }
+        $uri = "$path_base.$class_id.ch.fits";
+        my $command = "$destreak_command --magic_ds_id $imfile->{magic_ds_id}"
+            . " --exp_id $imfile->{exp_id}"
+            . " --stage_id $chip_id"
+            . " --component $imfile->{class_id}"
+            . " --cam_path_base $cam_path_base"
+            . " --streaks $streaks"
+            . " --path_base $path_base"
+            . " --uri $uri"
+            . " --no-update"
+            
+            ;
+
+        print "$command\n";
+        system $command;
+    }
+    if (!$processed) {
+        print STDERR "no images destreaked for $chip_id\n";
+        exit 1;
+    }
+} elsif ($warp_id) {
+    $stage = "warp";
+
+    $query = 
+    
+"SELECT
+    exp_id,
+    warp_id,
+    warpSkyfile.skycell_id,
+    warpSkyfile.magicked,
+    warpSkyfile.data_state,
+    magicDSRun.magic_ds_id,
+    magicMask.uri AS streaks_uri,
+    warpSkyfile.path_base,
+    magicDSFile.backup_path_base
+    FROM warpRun 
+    JOIN warpSkyfile using(warp_id)
+    JOIN magicDSRun ON stage = 'warp' AND stage_id = warpRun.warp_id 
+    JOIN magicDSFile ON magicDSRun.magic_ds_id = magicDSFile.magic_ds_id
+                        AND skycell_id = component
+    JOIN magicRun using(magic_id)
+    JOIN magicMask using(magic_id)
+    WHERE warpSkyfile.quality = 0
+        AND warpSkyfile.data_state = 'full'
+        AND warp_id = $warp_id";
+
+    $query .= " AND skycell_id = '$component'" if $component;
+
+    print "$query\n" if $verbose;
+
+    $stmt = $dbh->prepare($query);
+    $stmt->execute();
+
+    $destreak_command .= " --stage warp ";
+    my $num_rows = 0;
+    while (my $imfile = $stmt->fetchrow_hashref()) {
+        $num_rows++;
+        my $skycell_id = $imfile->{skycell_id};
+        my $path_base = $imfile->{path_base};
+        my $magicked = $imfile->{magicked};
+        my $streaks = $imfile->{streaks_uri};
+        my $uri;
+        if ($magicked > 0) {
+            # get source of image from "backup"
+#            my $dirname = dirname($path_base);
+#            my $base = basename($path_base);
+#            $path_base = $dirname . "/SR_" . $base;
+            $path_base = $imfile->{backup_path_base};
+        }
+        $uri = "$path_base.fits";
+        my $command = "$destreak_command --magic_ds_id $imfile->{magic_ds_id}"
+            . " --exp_id $imfile->{exp_id}"
+            . " --stage_id $warp_id"
+            . " --component $skycell_id"
+            . " --streaks $streaks"
+            . " --path_base $path_base"
+            . " --uri $uri"
+            . " --no-update"
+        ;
+
+        print "$command\n";
+        system $command;
+    }
+    if (!$num_rows) {
+        print STDERR "query returned no rows for warp_id: $warp_id\n";
+        exit 1;
+    }
+} else {
+    die "only implemented for chip and warp as yet";
+}
+
+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;
+}
+