Raw content of Bio::EnsEMBL::Pipeline::BatchSubmission::Local
<![CDATA[package Bio::EnsEMBL::Pipeline::BatchSubmission::Local;
use Bio::EnsEMBL::Utils::Exception qw(verbose throw warning info);
use Bio::EnsEMBL::Pipeline::BatchSubmission;
use vars qw(@ISA);
use strict;
use File::Copy;
@ISA = qw(Bio::EnsEMBL::Pipeline::BatchSubmission);
sub new{
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
$self->{'commandline'} = undef;
return $self;
}
sub construct_command_line{
my($self, $command) = @_;
if(!$command){
throw("Can't create command line if not command is passed in");
}
$self->command($command);
my $command_line = $command;
$command .= " 1> ".$self->temp_stdout." ";
$command .= "2> ".$self->temp_stderr." ";
$self->command($command);
}
sub open_command_line{
my ($self, $verbose) = @_;
if($verbose){
print STDERR "Opening ".$self->command."\n";
}
eval{
system($self->command);
};
if($@){
throw("FAILED to open commandline locally $@");
}
eval{
if($self->stderr_file){
$self->copy_output($self->temp_stderr, $self->stderr_file);
}
if($self->stdout_file){
$self->copy_output($self->temp_stdout, $self->stdout_file);
}
};
if($@){
throw("FAILED to copy output to defined location $@ keeping temporary".
"output")
}else{
$self->delete_temp_output;
}
}
sub copy_output{
my ($self, $file_to_copy, $new_location) = @_;
eval{
copy($file_to_copy, $new_location);
};
if($@){
throw("Copy of temporary output ".$file_to_copy." to new location ".
$new_location." failed $@");
}
return $new_location;
}
sub delete_temp_output{
my ($self) = @_;
if(-e $self->temp_stderr){
unlink $self->temp_stderr;
}
if(-e $self->temp_stdout){
unlink $self->temp_stdout;
}
}
sub temp_stderr{
my ($self, $file) = @_;
if($file){
$self->{'temp_stderr'} = $file;
}
if(!$self->{'temp_stderr'}){
my $num = int(rand(100000));
$self->{'temp_stderr'} = "/tmp/temp_local_out.".$num.".$$.err";
}
return $self->{'temp_stderr'};
}
sub temp_stdout{
my ($self, $file) = @_;
if($file){
$self->{'temp_stdout'} = $file;
}
if(!$self->{'temp_stdout'}){
my $num = int(rand(100000));
$self->{'temp_stdout'} = "/tmp/temp_local_out.".$num.".$$.out";
}
return $self->{'temp_stdout'};
}
sub job_stats{
my ($self) = @_;
my $hash = {};
$hash->{1} = 1;
return $hash;
}
sub temp_filename{
my ($self) = @_;
return '/tmp/';
}
]]>