From acb18be41a99ffdce50f53b6d32c8fe22492ab28 Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Thu, 21 Jun 2012 09:49:52 +0000
Subject: [PATCH] Die if we had no files
---
modules/Bio/EnsEMBL/Pipeline/FASTA/ConcatFiles.pm | 14 ++++++++------
1 file changed, 8 insertions(+), 6 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Pipeline/FASTA/ConcatFiles.pm b/modules/Bio/EnsEMBL/Pipeline/FASTA/ConcatFiles.pm
index 8f9959f2ce..099d43621c 100644
--- a/modules/Bio/EnsEMBL/Pipeline/FASTA/ConcatFiles.pm
+++ b/modules/Bio/EnsEMBL/Pipeline/FASTA/ConcatFiles.pm
@@ -52,7 +52,6 @@ use strict;
use warnings;
use base qw/Bio::EnsEMBL::Pipeline::FASTA::Base/;
-use Bio::EnsEMBL::Utils::Exception qw/throw/;
use File::Spec;
sub param_defaults {
@@ -91,14 +90,14 @@ sub run {
if(-f $target_file) {
$self->info("Target already exists. Removing");
- unlink $target_file or throw "Could not remove $target_file: $!";
+ unlink $target_file or $self->throw("Could not remove $target_file: $!");
}
$self->info('Running concat');
foreach my $file (@file_list) {
$self->fine('Processing %s', $file);
system("cat $file >> $target_file")
- and throw sprintf('Cannot concat %s into %s. RC %d', $file, $target_file, ($?>>8));
+ and $self->throw( sprintf('Cannot concat %s into %s. RC %d', $file, $target_file, ($?>>8)));
}
$self->info("Catted files together");
@@ -106,14 +105,17 @@ sub run {
$self->param('target_file', $target_file);
}
else {
- $self->info("No files found so nothing to concat");
+ $self->throw("Cannot continue as we found no files to concat");
}
return;
}
sub write_output {
my ($self) = @_;
- $self->dataflow_output_id({ file => $self->param('target_file'), species => $self->param('species') }, 1);
+ my $file = $self->param('target_file');
+ if($file) {
+ $self->dataflow_output_id({ file => $file, species => $self->param('species') }, 1);
+ }
return;
}
@@ -123,7 +125,7 @@ sub get_dna_files {
my $data_type = $self->param('data_type');
my $regex_hash = $self->param($data_type);
if(! $regex_hash ) {
- throw "We do not have an entry for the data_type $data_type in our regex lookup hash. Edit this module";
+ $self->throw("We do not have an entry for the data_type $data_type in our regex lookup hash. Edit this module");
}
my $regex = $regex_hash->{regex};
my $filter = sub {
--
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