lib/CXGN/Fieldbook/DownloadTrial.pm

   1 package CXGN::Fieldbook::DownloadTrial;
   2
   3 use Moose;
   4 use Moose::Util::TypeConstraints;
   5 use Try::Tiny;
   6 use File::Basename qw | basename dirname|;
   7 use File::Copy;
   8 use File::Spec::Functions;
   9 use Digest::MD5;
  10 use CXGN::List::Validate;
  11 use Data::Dumper;
  12 use CXGN::Trial::TrialLayout;
  13 use Spreadsheet::WriteExcel;
  14 use CXGN::Trait;
  15 use CXGN::List::Transform;
  16 use CXGN::People::Person;
  17 use DateTime;
  18
  19 has 'bcs_schema' => (
  20     isa => "Bio::Chado::Schema",
  21     is => 'ro',
  22     required => 1,
  23 );
  24
  25 has 'metadata_schema' => (
  26     isa => "CXGN::Metadata::Schema",
  27     is => 'ro',
  28     required => 1,
  29 );
  30
  31 has 'phenome_schema' => (
  32     isa => "CXGN::Phenome::Schema",
  33     is => 'ro',
  34     required => 1,
  35 );
  36
  37 has 'trial_id'   => (
  38     isa => "Int",
  39     is => 'ro',
  40     required => 1,
  41 );
  42
  43 has 'tempfile' => (isa => 'Str', is => 'ro',
  44     predicate => 'has_tempfile',
  45     required => 1,
  46 );
  47
  48 has 'archive_path' => (isa => 'Str', is => 'ro',
  49     predicate => 'has_archive_path',
  50     required => 1,
  51 );
  52
  53 has 'user_id' => (
  54     is => 'ro',
  55     isa => 'Int',
  56     required => 1,
  57 );
  58
  59 has 'user_name' => (
  60     is => 'ro',
  61     isa => 'Str',
  62     required => 1,
  63 );
  64
  65 has 'file_metadata' => (isa => 'Str', is => 'rw', predicate => 'has_file_metadata');
  66
  67
  68 sub download {
  69     my $self = shift;
  70     my %errors;
  71     my @error_messages;
  72
  73     my $schema = $self->bcs_schema();
  74     my $trial_id = $self->trial_id();
  75     my $tempfile = $self->tempfile();
  76     my $wb = Spreadsheet::WriteExcel->new($tempfile);
  77     if (!$wb) {
  78         push @error_messages, "Could not create file.";
  79         $errors{'error_messages'} = \@error_messages;
  80         return \%errors;
  81     }
  82
  83     my $ws = $wb->add_worksheet();
  84     my $trial_layout;
  85     print STDERR "\n\nTrial id: ($trial_id)\n\n";
  86     try {
  87         $trial_layout = CXGN::Trial::TrialLayout->new({schema => $schema, trial_id => $trial_id} );
  88     };
  89     if (!$trial_layout) {
  90         push @error_messages, "Trial does not have valid field design.";
  91         $errors{'error_messages'} = \@error_messages;
  92         return \%errors;
  93     }
  94
  95     my $trial_name =  $trial_layout->get_trial_name();
  96     $ws->write(0, 0, 'plot_id');
  97     $ws->write(0, 1, 'range');
  98     $ws->write(0, 2, 'plot');
  99     $ws->write(0, 3, 'rep');
 100     $ws->write(0, 4, 'accession');
 101     $ws->write(0, 5, 'is_a_control');
 102
 103     my %design = %{$trial_layout->get_design()};
 104     my $row_num = 1;
 105     foreach my $key (sort { $a <=> $b} keys %design) {
 106     my %design_info = %{$design{$key}};
 107     $ws->write($row_num,0,$design_info{'plot_name'});
 108     $ws->write($row_num,1,$design_info{'block_number'});
 109     $ws->write($row_num,2,$design_info{'plot_number'});
 110     $ws->write($row_num,3,$design_info{'rep_number'});
 111     $ws->write($row_num,4,$design_info{'accession_name'});
 112     $ws->write($row_num,5,$design_info{'is_a_control'});
 113     $row_num++;
 114     }
 115     $wb->close();
 116
 117     my $user_id = $self->user_id();
 118     open(my $F, "<", $tempfile) || die "Can't open file ".$self->tempfile();
 119         binmode $F;
 120         my $md5 = Digest::MD5->new();
 121         $md5->addfile($F);
 122     close($F);
 123
 124     my $project = $trial_layout->get_project;
 125
 126     my $time = DateTime->now();
 127     my $timestamp = $time->ymd()."_".$time->hms();
 128     my $user_name = $self->user_name();
 129     my $subdirectory_name = "tablet_field_layout";
 130     my $archived_file_name = catfile($user_id, $subdirectory_name,$timestamp."_".$project->name.".xls");
 131     my $archive_path = $self->archive_path();
 132     my $file_destination =  catfile($archive_path, $archived_file_name);
 133
 134     if (!-d $archive_path) {
 135         mkdir $archive_path;
 136     }
 137
 138     if (! -d catfile($archive_path, $user_id)) {
 139         mkdir (catfile($archive_path, $user_id));
 140     }
 141
 142     if (! -d catfile($archive_path, $user_id,$subdirectory_name)) {
 143         mkdir (catfile($archive_path, $user_id, $subdirectory_name));
 144     }
 145
 146     my $metadata_schema = $self->metadata_schema();
 147     my $md_row = $metadata_schema->resultset("MdMetadata")->create({
 148         create_person_id => $user_id,
 149     });
 150     $md_row->insert();
 151
 152     my $file_row = $metadata_schema->resultset("MdFiles")->create({
 153         basename => basename($file_destination),
 154         dirname => dirname($file_destination),
 155         filetype => 'tablet field layout xls',
 156         md5checksum => $md5->hexdigest(),
 157         metadata_id => $md_row->metadata_id(),
 158     });
 159     $file_row->insert();
 160
 161     my $field_layout_cvterm = SGN::Model::Cvterm->get_cvterm_row($schema, 'field_layout', 'experiment_type' );
 162
 163     my $experiment = $schema->resultset('NaturalDiversity::NdExperiment')->find(
 164         {
 165             'nd_experiment_projects.project_id' => $project->project_id,
 166             type_id => $field_layout_cvterm->cvterm_id(),
 167         },
 168         {
 169             join => 'nd_experiment_projects',
 170         }
 171     );
 172
 173     my $phenome_schema = $self->phenome_schema();
 174     my $experiment_files = $phenome_schema->resultset("NdExperimentMdFiles")->create({
 175         nd_experiment_id => $experiment->nd_experiment_id(),
 176         file_id => $file_row->file_id(),
 177     });
 178     $experiment_files->insert();
 179
 180     move($tempfile,$file_destination);
 181     unlink $tempfile;
 182
 183     my $result = $file_row->file_id;
 184     return {result => $result, file => $file_destination};
 185 }
 186
 187 1;