Index: /trunk/tools/runchipimfile.pl =================================================================== --- /trunk/tools/runchipimfile.pl (revision 29586) +++ /trunk/tools/runchipimfile.pl (revision 29586) @@ -0,0 +1,186 @@ +#!/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 ($first, $last, $stage, $alt_workdir, $no_verbose); + +my $dbname = "gpc1"; +my ($chip_id, $class_id, $threads, $update, $redirect, $pretend, $save_temps); + +GetOptions( + 'chip_id=i' => \$chip_id, + 'class_id=s' => \$class_id, + 'threads=i' => \$threads, + 'pretend' => \$pretend, + 'redirect-output' => \$redirect, + 'update' => \$update, + 'dbname=s' => \$dbname, + 'no-verbose' => \$no_verbose, + 'save-temps' => \$save_temps, +) or pod2usage( 2 ); + +pod2usage( -msg => "Unknown option: @ARGV", -exitval => 2 ) if @ARGV; +pod2usage( -msg => "--chip_id and --class_id are required", -exitval => 2 ) + if !$chip_id or !$class_id; + +my $ipprc = PS::IPP::Config->new(); +my $dbh = getDBHandle(); + +my $query1 = "SELECT chipProcessedImfile.path_base, camera, exp_id, rawImfile.magicked AS raw_magicked, (rawImfile.user_1 is not NULL and rawImfile.user_1 > 0.5) As deburned, chip_imfile_id, chipProcessedImfile.fault, rawImfile.uri, chipRun.reduction, chipRun.state"; +$query1 .= " FROM chipRun join chipProcessedImfile using(chip_id) JOIN chipImfile USING (chip_id, class_id) JOIN rawExp using(exp_id) JOIN rawImfile USING(exp_id) WHERE chip_id = $chip_id AND class_id = $class_id"; + +my $stmt1 = $dbh->prepare($query1); +$stmt1->execute(); +my $results = $stmt1->fetchrow_hashref(); +die "query returned no results\n" if !$results; +my $path_base = $results->{path_base}; +my $chip_imfile_id = $results->{chip_imfile_id}; +my $reduction = $results->{reduction}; +my $magicked = $results->{raw_magicked}; +my $camera = $results->{camera}; +my $state = $results->{state}; +my $fault = $results->{fault}; +my $uri = $results->{uri}; +my $deburned = $results->{deburned}; +my $exp_id = $results->{exp_id}; + +notdone + +die "cannot update database for a chip that is not faulted\n" if $update and !$fault; + +die "path_base not found\n" if !$path_base; +die "chip_imfile_id not found\n" if !$chip_imfile_id; +die "magicked not found\n" if ! defined $magicked; +die "camera not found\n" if !$camera; +die "state not found\n" if !$state; + +my $run_state; +if ($state eq 'full' or $state eq 'new') { + $run_state = 'new'; +} elsif ($state eq 'update') { + $state = 'update'; +} else { + die "unexpected warpRun.state found: $state\n"; +} + +my $command = "chip_imfile.pl --exp_id $exp_id --chip_id $chip_id --class_id $class_id --chip_imfile_id $chip_imfile_id --uri $uri --camera $camera --run-state $run_state --deburned $deburned --outroot $path_base" ; + +$command .= " --magicked $magicked" if $magicked > 0; +$command .= " --reduction $reduction" if $reduction and ($reduction ne "NULL"); +$command .= " --redirect-output" if $redirect; +$command .= " --save-temps" if $save_temps; +$command .= " --no-update" unless $update; +$command .= " --verbose" unless $no_verbose; +$command .= " --dbname $dbname" if $dbname; + + +if ($update) { + my $revert_command = "chiptool -revertprocessedimfile -chip_id $chip_id -class_id $class_id -dbname $dbname"; + if ($pretend) { + print "skipping $revert_command\n"; + } else { + my $rc = system $revert_command; + if ($rc != 0) { + my $status = $rc >> 8; + print STDERR "$revert_command failed: $rc $status\n"; + exit $status; + } + } +} +print "command to process this skycell\n"; +print "$command\n"; + +exit 0 if $pretend; + +exit system $command; + + +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 + +runchipimfile.pl - gather the parameters for and execute chip_imfile.pl + +=head1 SYNOPSIS + + XXX: pod TODO + + perl runwarpskyfile.pl --warp_id --skycell_id [--threads ] [--update] [--redirect-output] [--pretend] [--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 + +The id of the warpSkyfile run to process. + +=item * --skycell_id + +The skycell_id of the warpSkyfile run to process. + +=item * --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 + +Name of the IPP databse to query. Default is 'gpc1'. +Optional. + + +=head1 SEE ALSO +L, L, L + +=cut