lib/CXGN/Trial/Download.pm

   1
   2 package CXGN::Trial::Download;
   3
   4 use Moose;
   5
   6 use Moose::Util::TypeConstraints;
   7 use Try::Tiny;
   8 use File::Basename qw | basename dirname|;
   9 use Digest::MD5;
  10 use CXGN::List::Validate;
  11 use Data::Dumper;
  12 use CXGN::Trial;
  13 use CXGN::Trial::TrialLayout;
  14 use Spreadsheet::WriteExcel;
  15 use CXGN::Trait;
  16 use CXGN::List::Transform;
  17 use CXGN::People::Person;
  18 use DateTime;
  19
  20 with 'MooseX::Object::Pluggable';
  21
  22
  23 has 'bcs_schema' => (
  24     isa => "Bio::Chado::Schema",
  25     is => 'ro',
  26     required => 1,
  27     );
  28
  29 has 'trial_id'   => (
  30     isa => "Int",
  31     is => 'ro',
  32     required => 1,
  33     );
  34
  35
  36 has 'bcs_schema' => (
  37     is       => 'ro',
  38     isa      => 'DBIx::Class::Schema',
  39     required => 1,
  40     );
  41
  42 # can be provided for logging purposes
  43 has 'user_id' => (
  44     is => 'ro',
  45     isa => 'Int',
  46     );
  47
  48 has 'trial_download_logfile' => (
  49     is => 'ro',
  50     isa => 'Str',
  51     );
  52
  53 ## defines the plugin with which the download will be processed
  54 has 'format' => (isa => 'Str', is => 'ro', required => 1);
  55
  56 has 'data_level' => (isa => 'Str | Undef', is => 'ro', default => 'plots');
  57
  58 has 'sample_number' => (isa => 'Int | Undef', is => 'ro', default => 0);
  59
  60 has 'predefined_columns' => (isa => 'ArrayRef[HashRef] | Undef', is => 'ro');
  61
  62 has 'trait_list' => (isa => 'ArrayRef', is => 'rw', predicate => 'has_trait_list' );
  63
  64 has 'filename' => (isa => 'Str', is => 'ro',
  65                    predicate => 'has_filename',
  66                    required => 1,
  67                   );
  68
  69 has 'file_metadata' => (isa => 'Str', is => 'rw', predicate => 'has_file_metadata');
  70
  71 ## used when downloading phenotypes as either csv or xls.
  72 has 'include_timestamp' => (isa => 'Bool', is => 'ro', default => 0);
  73
  74
  75 sub BUILD {
  76     my $self = shift;
  77     $self->load_plugin($self->format());
  78 }
  79
  80 # sub verify {
  81 #     my $self = shift;
  82
  83 #     $self->load_plugin($self->format());
  84
  85 #     return $self->plugin_verify();
  86 # }
  87
  88 # sub download {
  89 #     my $self = shift;
  90
  91 #     print STDERR "Format: ".$self->format()."\n";
  92 #     eval {
  93 #       $self->load_plugin($self->format());
  94 #     };
  95 #     if ($@) {
  96 #       die "The plugin specified (".$self->format().") for the download does not exist";
  97 #     }
  98
  99 #     my $error = $self->plugin_download();
 100
 101 #     return $error;
 102 # }
 103
 104 sub trial_download_log {
 105     my $self = shift;
 106     my $trial_id = shift;
 107     my $message = shift;
 108
 109     if (! $self->user_id && !$self->trial_download_logfile()) {
 110         return;
 111     }
 112     else {
 113         print STDERR "Note: set config variable trial_download_logfile to obtain a log of downloaded trials.\n";
 114     }
 115
 116     my $now = DateTime->now();
 117
 118     open (my $F, ">>", $self->trial_download_logfile()) || die "Can't open ".$self->trial_download_logfile();
 119     my $username = CXGN::People::Person->new($self->bcs_schema->storage->dbh(), $self->user_id())->get_username();
 120     print $F join("\t", (
 121                       $username,
 122                       $trial_id,
 123                       $message,
 124                       $now->year()."-".$now->month()."-".$now->day()." ".$now->hour().":".$now->minute()));
 125     print $F "\n";
 126
 127     close($F);
 128
 129
 130 }
 131
 132
 133 1;