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0
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1 =pod
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2
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3 =head1 LICENSE
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4
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5 Copyright (c) 1999-2012 The European Bioinformatics Institute and
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6 Genome Research Limited. All rights reserved.
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7
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8 This software is distributed under a modified Apache license.
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9 For license details, please see
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10
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11 http://www.ensembl.org/info/about/code_licence.html
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12
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13 =head1 CONTACT
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14
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15 Please email comments or questions to the public Ensembl
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16 developers list at <dev@ensembl.org>.
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17
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18 Questions may also be sent to the Ensembl help desk at
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19 <helpdesk@ensembl.org>.
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20
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21 =head1 NAME
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22
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23 Bio::EnsEMBL::Pipeline::ChecksumGenerator
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24
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25 =head1 DESCRIPTION
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26
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27 Creates a CHECKSUMS file in the given directory which is produced from running
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28 the sum command over every file in the directory. This excludes the CHECKSUMS
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29 file, parent directory or any hidden files.
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30
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31 Allowed parameters are:
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32
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33 =over 8
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34
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35 =item dir - The directory to generate checksums for
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36
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37 =item gzip - If the resulting file should be gzipped. Defaults to false
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38
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39 =back
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40
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41 =cut
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42
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43 package Bio::EnsEMBL::Pipeline::ChecksumGenerator;
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44
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45 use strict;
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46 use warnings;
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47
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48 use base qw/Bio::EnsEMBL::Pipeline::Base/;
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49
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50 use File::Spec;
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51 use Bio::EnsEMBL::Utils::IO qw/work_with_file gz_work_with_file/;
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52
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53 sub param_defaults {
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54 my ($self) = @_;
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55 return {
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56 gzip => 0
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57 };
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58 }
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59
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60 sub fetch_input {
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61 my ($self) = @_;
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62 my $dir = $self->param('dir');
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63 $self->throw("No 'dir' parameter specified") unless $dir;
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64 $self->throw("Dir $dir does not exist") unless -d $dir;
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65 return;
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66 }
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67
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68 sub run {
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69 my ($self) = @_;
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70 my @checksums;
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71
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72 my $dir = $self->param('dir');
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73 $self->info('Checksumming directory %s', $dir);
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74
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75 opendir(my $dh, $dir) or die "Cannot open directory $dir";
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76 my @files = sort { $a cmp $b } readdir($dh);
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77 closedir($dh) or die "Cannot close directory $dir";
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78
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79 foreach my $file (@files) {
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80 next if $file =~ /^\./; #hidden file or up/current dir
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81 next if $file =~ /^CHECKSUM/;
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82 my $path = File::Spec->catfile($dir, $file);
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83 my $checksum = $self->checksum($path);
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84 push(@checksums, [$checksum, $file])
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85 }
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86
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87 $self->param('checksums', \@checksums);
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88 return;
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89 }
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90
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91 sub write_output {
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92 my ($self) = @_;
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93 my $dir = $self->param('dir');
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94 my $checksum = File::Spec->catfile($dir, 'CHECKSUMS');
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95 $checksum .= '.gz' if $self->param('gzip');
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96 if(-f $checksum) {
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97 $self->info('Checksum file already exists. Removing');
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98 unlink $checksum;
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99 }
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100
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101 my @checksums = @{$self->param('checksums')};
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102
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103 return unless @checksums;
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104
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105 my $writer = sub {
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106 my ($fh) = @_;
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107 foreach my $entry (@checksums) {
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108 my $line = join(qq{\t}, @{$entry});
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109 print $fh $line;
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110 print $fh "\n";
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111 }
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112 return;
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113 };
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114 my @params = ($checksum, 'w', $writer);
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115
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116
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117 if($self->param('gzip')) {
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118 gz_work_with_file(@params);
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119 }
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120 else {
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121 work_with_file(@params);
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122 }
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123
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124 $self->permissions($checksum);
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125 return;
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126 }
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127
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128 sub checksum {
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129 my ($self, $path) = @_;
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130 my $checksum = `sum $path`;
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131 $checksum =~ s/\s* $path//xms;
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132 chomp($checksum);
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133 return $checksum;
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134 }
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135
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136 sub permissions {
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137 my ($self, $file) = @_;
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138 my $mode = 0666;
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139 chmod($mode, $file) or $self->throw("Cannot perform the chmod to mode $mode for file $file");
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140 return;
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141 }
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142
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143 1;
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