lib/CXGN/UploadFile.pm

   1 package CXGN::UploadFile;
   2
   3 =head1 NAME
   4
   5 CXGN::UploadFile - an object to handle uploading files
   6
   7 =head1 USAGE
   8
   9  my $uploader = CXGN::UploadFile->new({
  10     tempfile => '/tmp/myfile.csv',
  11     subdirectory => 'some_directory',
  12     second_subdirectory => 'some_directory',
  13     archive_path => '/some/path/to/dir',
  14     archive_filename => 'myfilename.csv',
  15     timestamp => '2016-09-24_10:30:30',
  16     user_id => 41,
  17     user_role => 'curator'
  18  });
  19  my $uploaded_file = $uploader->archive();
  20  my $md5 = $uploader->get_md5($uploaded_file);
  21
  22  In this example, the tempfile myfile.csv will be saved in: /some/path/to/dir/41/some_directory/2016-09-24_10:30:30_myfilename.csv
  23
  24 =head1 DESCRIPTION
  25
  26
  27 =head1 AUTHORS
  28
  29  Jeremy D. Edwards (jde22@cornell.edu)
  30
  31 =cut
  32
  33 use strict;
  34 use warnings;
  35 use Moose;
  36 use Try::Tiny;
  37 use List::MoreUtils qw /any /;
  38 use File::Copy;
  39 use File::Spec::Functions;
  40 use File::Basename qw | basename dirname|;
  41 use Digest::MD5;
  42 use Data::Dumper;
  43
  44 has 'tempfile' => (isa => "Str",
  45     is => 'rw',
  46     required => 0
  47 );
  48
  49 has 'subdirectory' => (isa => "Str",
  50     is => 'rw',
  51     required => 0
  52 );
  53
  54 has 'second_subdirectory' => (isa => "Str",
  55     is => 'rw',
  56     required => 0
  57 );
  58
  59 has 'third_subdirectory' => (isa => "Str",
  60     is => 'rw',
  61     required => 0
  62 );
  63
  64 has 'archive_path' => (isa => "Str",
  65     is => 'rw',
  66     required => 0
  67 );
  68
  69 has 'archive_filename' => (isa => "Str",
  70     is => 'rw',
  71     required => 0
  72 );
  73
  74 has 'timestamp' => (isa => "Str",
  75     is => 'rw',
  76     required => 0
  77 );
  78
  79 has 'user_id' => (isa => "Int",
  80     is => 'rw',
  81     required => 0
  82 );
  83
  84 has 'user_role' => (isa => "Str",
  85     is => 'rw',
  86     required => 0
  87 );
  88
  89 has 'include_timestamp' => (
  90     isa => "Bool",
  91     is => 'rw',
  92     required => 0,
  93     default => 1
  94 );
  95
  96 sub archive {
  97     my $self = shift;
  98     my $subdirectory = $self->subdirectory;
  99     my $second_subdirectory = $self->second_subdirectory;
 100     my $third_subdirectory = $self->third_subdirectory;
 101     my $tempfile = $self->tempfile;
 102     my $archive_filename = $self->archive_filename;
 103     my $timestamp = $self->timestamp;
 104     my $archive_path = $self->archive_path;
 105     my $user_id = $self->user_id;
 106     my $file_destination;
 107     my $error;
 108
 109     #    if (!$subdirectory || !$tempfile || !$archive_filename || !$timestamp || !$archive_path || !$user_id){
 110     if (!$subdirectory || !$tempfile || !$timestamp || !$user_id){
 111         die "To archive a tempfile you need to provide: tempfile, subdirectory, archive_filename, timestamp, archive_path, and user_id\n";
 112     }
 113
 114     if (!any { $_ eq "curator" || $_ eq "submitter" || $_ eq "sequencer" } ($self->user_role)  ) {
 115         die  "You have insufficient privileges to archive a file.\n". Dumper $self->user_role;
 116     }
 117     # if (!$subdirectory || !$tempfile || !$archive_filename ) {
 118     #     print STDERR "File archive failed: incomplete information to archive file.\n";
 119     #   die "File archive failed: incomplete information to archive file.\n";
 120     # }
 121     if ($self->include_timestamp){
 122         $file_destination =  catfile($archive_path, $user_id, $subdirectory, $timestamp."_".$archive_filename);
 123     }
 124     else {
 125         $file_destination =  catfile($archive_path, $user_id, $subdirectory, $archive_filename);
 126     }
 127     if ($second_subdirectory) {
 128         if ($self->include_timestamp){
 129             $file_destination =  catfile($archive_path, $user_id, $subdirectory, $second_subdirectory, $timestamp."_".$archive_filename);
 130         }
 131         else {
 132             $file_destination =  catfile($archive_path, $user_id, $subdirectory, $second_subdirectory, $archive_filename);
 133         }
 134         if ($third_subdirectory) {
 135             if ($self->include_timestamp){
 136                 $file_destination =  catfile($archive_path, $user_id, $subdirectory, $second_subdirectory, $third_subdirectory, $timestamp."_".$archive_filename);
 137             }
 138             else {
 139                 $file_destination =  catfile($archive_path, $user_id, $subdirectory, $second_subdirectory, $third_subdirectory, $archive_filename);
 140             }
 141         }
 142     }
 143
 144     try {
 145         if (!-d $archive_path) {
 146             mkdir $archive_path;
 147         }
 148         if (! -d catfile($archive_path, $user_id)) {
 149             mkdir (catfile($archive_path, $user_id));
 150         }
 151         if (! -d catfile($archive_path, $user_id, $subdirectory)) {
 152             mkdir (catfile($archive_path, $user_id, $subdirectory));
 153         }
 154         if ($second_subdirectory) {
 155             if (! -d catfile($archive_path, $user_id, $subdirectory, $second_subdirectory)) {
 156                 mkdir (catfile($archive_path, $user_id, $subdirectory, $second_subdirectory));
 157             }
 158         }
 159         if ($second_subdirectory && $third_subdirectory) {
 160             if (! -d catfile($archive_path, $user_id, $subdirectory, $second_subdirectory, $third_subdirectory)) {
 161                 mkdir (catfile($archive_path, $user_id, $subdirectory, $second_subdirectory, $third_subdirectory));
 162             }
 163         }
 164
 165         copy($tempfile,$file_destination);
 166     }
 167     catch {
 168         $error = "Error saving archived file: $file_destination\n$_";
 169     };
 170     if ($error) {
 171         print STDERR  "$error\n";
 172     }
 173     print STDERR "ARCHIVED: $file_destination\n";
 174     return $file_destination;
 175 }
 176
 177 sub get_md5 {
 178     my $self = shift;
 179     my $file_name_and_location = shift;
 180     #print STDERR $file_name_and_location;
 181
 182     open(my $F, "<", $file_name_and_location) || die "Can't open file $file_name_and_location";
 183     binmode $F;
 184     my $md5 = Digest::MD5->new();
 185     $md5->addfile($F);
 186     close($F);
 187     return $md5;
 188 }
 189
 190 ###
 191 1;
 192 ###