lib/CXGN/Trial/Download.pm

   1
   2 package CXGN::Trial::Download;
   3
   4 =head1 NAME
   5
   6 CXGN::Trial::Download
   7
   8 =head1 SYNOPSIS
   9
  10 This module loads one of the plugins in /CXGN/Trial/Download/Plugin/
  11 This module is used differently depending on the plugin.
  12 Example usage for all plugins is listed here.
  13
  14 ------------------------------------------------------------------
  15
  16 For downloading trial(s) xls spreadsheet for collecting phenotypes (as used
  17 from SGN::Controller::AJAX::PhenotypesDownload->create_phenotype_spreadsheet):
  18
  19 my $rel_file = $c->tempfile( TEMPLATE => 'download/downloadXXXXX');
  20 my $tempfile = $c->config->{basepath}."/".$rel_file.".xls";
  21 my $create_spreadsheet = CXGN::Trial::Download->new({
  22     bcs_schema => $schema,
  23     trial_list => \@trial_id_list,
  24     trait_list => \@trait_list,
  25     filename => $tempfile,
  26     format => "ExcelBasic",
  27     data_level => $data_level,
  28     sample_number => $sample_number,
  29     predefined_columns => $predefined_columns,
  30 });
  31 $create_spreadsheet->download();
  32 $c->stash->{rest} = { filename => $urlencode{$rel_file.".xls"} };
  33
  34 ------------------------------------------------------------------
  35
  36 For downloading phenotypes in a matrix where columns contain the phenotypes
  37 and rows contain the observation unit (as used from
  38 SGN::Controller::BreedersToolbox::Download->download_phenotypes_action which
  39 is used from the wizard, trial detail page, and manage trials page for
  40 downlading phenotypes):
  41
  42 There a number of optional keys for filtering down the phenotypes
  43 (trait_list, year_list, location_list, etc). Keys can be entirely ignored
  44 if you don't need to filter by them.
  45
  46 As a CSV:
  47 my $plugin = 'TrialPhenotypeCSV';
  48
  49 As a xls:
  50 my $plugin = 'TrialPhenotypeExcel';
  51
  52 my $download = CXGN::Trial::Download->new({
  53     bcs_schema => $schema,
  54     trait_list => \@trait_list_int,
  55     year_list => \@year_list,
  56     location_list => \@location_list_int,
  57     trial_list => \@trial_list_int,
  58     accession_list => \@accession_list_int,
  59     plot_list => \@plot_list_int,
  60     plant_list => \@plant_list_int,
  61     filename => $tempfile,
  62     format => $plugin,
  63     data_level => $data_level,
  64     include_timestamp => $timestamp_option,
  65     exclude_phenotype_outlier => $exclude_phenotype_outlier,
  66     trait_contains => \@trait_contains_list,
  67     phenotype_min_value => $phenotype_min_value,
  68     phenotype_max_value => $phenotype_max_value,
  69     has_header=>$has_header
  70 });
  71 my $error = $download->download();
  72 my $file_name = "phenotype.$format";
  73 $c->res->content_type('Application/'.$format);
  74 $c->res->header('Content-Disposition', qq[attachment; filename="$file_name"]);
  75 my $output = read_file($tempfile);
  76 $c->res->body($output);
  77
  78 --------------------------------------------------------------------------
  79
  80 For downloading a "DataCollector Spreadsheet" for collecting phenotypes (as
  81 used in SGN::Controller::AJAX::DataCollectorDownload->create_DataCollector_spreadsheet_POST):
  82
  83 my $create_spreadsheet = CXGN::Trial::Download->new({
  84     bcs_schema => $schema,
  85     trial_id => $trial_id,
  86     trait_list => \@trait_list,
  87     filename => $file_path,
  88     format => 'DataCollectorExcel',
  89     data_level => $data_level,
  90 });
  91 my $spreadsheet_response = $create_spreadsheet->download();
  92 if ($spreadsheet_response->{error}) {
  93     $c->stash->{rest} = { error => $spreadsheet_response->{error} };
  94     return;
  95 }
  96 my $file_name = basename($file_path);
  97 $c->stash->{rest} = { filename => $urlencode{$tempfile.".xls"} };
  98
  99 -------------------------------------------------------------------------------
 100
 101 For downloading a trial's layout (as used from CXGN::Trial::Download->trial_download):
 102
 103 A trial's layout can optionally include treatment and phenotype summary
 104 information, mapping to treatment_project_ids and trait_list.
 105 These keys can be ignored if you don't need them in the layout.
 106
 107 As a XLS:
 108 my $plugin = "TrialLayoutExcel";
 109
 110 As a CSV:
 111 my $plugin = "TrialLayoutCSV";
 112
 113 my $download = CXGN::Trial::Download->new({
 114     bcs_schema => $schema,
 115     trial_id => $c->stash->{trial_id},
 116     trait_list => \@trait_list,
 117     filename => $tempfile,
 118     format => $plugin,
 119     data_level => $data_level,
 120     treatment_project_ids => \@treatment_project_ids,
 121     selected_columns => $selected_cols,
 122 });
 123 my $error = $download->download();
 124 my $file_name = $trial_id . "_" . "$what" . ".$format";
 125 $c->res->content_type('Application/'.$format);
 126 $c->res->header('Content-Disposition', qq[attachment; filename="$file_name"]);
 127 my $output = read_file($tempfile);
 128 $c->res->body($output);
 129
 130 ------------------------------------------------------------------------------
 131
 132 For downloading the IGD sequencing facility spreadsheet (as used from
 133 SGN::Controller::BreedersToolbox::Download->download_sequencing_facility_spreadsheet):
 134
 135 my $td = CXGN::Trial::Download->new({
 136     bcs_schema => $schema,
 137     trial_id => $trial_id,
 138     format => "IGDFacilitySpreadsheet",
 139     filename => $file_path,
 140     user_id => $c->user->get_object()->get_sp_person_id(),
 141     trial_download_logfile => $c->config->{trial_download_logfile},
 142 });
 143 $td->download();
 144 my $file_name = basename($file_path);
 145 $c->res->content_type('Application/xls');
 146 $c->res->header('Content-Disposition', qq[attachment; filename="$file_name"]);
 147 my $output = read_file($file_path, binmode=>':raw');
 148 $c->res->body($output);
 149
 150
 151 -------------------------------------------------------------------------------
 152
 153
 154 =head1 AUTHORS
 155
 156 =cut
 157
 158
 159 use Moose;
 160 use Moose::Util::TypeConstraints;
 161 use Try::Tiny;
 162 use File::Basename qw | basename dirname|;
 163 use Digest::MD5;
 164 use CXGN::List::Validate;
 165 use Data::Dumper;
 166 use CXGN::Trial;
 167 use CXGN::Trial::TrialLayout;
 168 use Spreadsheet::WriteExcel;
 169 use CXGN::Trait;
 170 use CXGN::List::Transform;
 171 use CXGN::People::Person;
 172 use DateTime;
 173
 174 with 'MooseX::Object::Pluggable';
 175
 176
 177 has 'bcs_schema' => (
 178     isa => "Bio::Chado::Schema",
 179     is => 'ro',
 180     required => 1,
 181     );
 182
 183 has 'trial_id'   => (
 184     isa => "Int",
 185     is => 'ro',
 186     );
 187
 188 # can be provided for logging purposes
 189 has 'user_id' => (
 190     is => 'ro',
 191     isa => 'Int',
 192     );
 193
 194 has 'trial_download_logfile' => (
 195     is => 'ro',
 196     isa => 'Str',
 197     );
 198
 199 ## defines the plugin with which the download will be processed
 200 has 'format' => (isa => 'Str', is => 'ro', required => 1);
 201 has 'data_level' => (isa => 'Str | Undef', is => 'ro', default => 'plots');
 202 has 'sample_number' => (isa => 'Int | Undef', is => 'ro', default => 0);
 203 has 'predefined_columns' => (isa => 'ArrayRef[HashRef] | Undef', is => 'ro');
 204 has 'trait_list' => (isa => 'ArrayRef[Int|Str]|Undef', is => 'rw', predicate => 'has_trait_list' );
 205 has 'trait_component_list' => (isa => 'ArrayRef[Int]|Undef', is => 'rw' );
 206 has 'trial_list' => (isa => 'ArrayRef[Int]|Undef', is => 'rw' );
 207 has 'accession_list' => (isa => 'ArrayRef[Int]|Undef', is => 'rw' );
 208 has 'plot_list' => (isa => 'ArrayRef[Int]|Undef', is => 'rw' );
 209 has 'plant_list' => (isa => 'ArrayRef[Int]|Undef', is => 'rw' );
 210 has 'location_list' => (isa => 'ArrayRef[Int]|Undef', is => 'rw' );
 211 has 'year_list' => (isa => 'ArrayRef[Int]|Undef', is => 'rw' );
 212 has 'include_timestamp' => (isa => 'Bool', is => 'ro', default => 0);
 213 has 'exclude_phenotype_outlier' => (isa => 'Bool', is => 'ro', default => 0);
 214 has 'has_header' => (isa => 'Bool', is => 'ro', default => 1);
 215 has 'trait_contains' => (isa => 'ArrayRef[Str]|Undef', is => 'rw');
 216 has 'phenotype_min_value' => (isa => 'Str', is => 'rw');
 217 has 'phenotype_max_value' => (isa => 'Str', is => 'rw');
 218 has 'search_type' => (isa => 'Str', is => 'rw');
 219 has 'treatment_project_ids' => (isa => 'ArrayRef[Int]|Undef', is => 'rw');
 220 has 'selected_columns' => (isa => 'HashRef|Undef', is => 'rw');
 221 has 'include_notes' => (isa => 'Str', is => 'rw');
 222 has 'filename' => (isa => 'Str', is => 'ro',
 223                    predicate => 'has_filename',
 224                    required => 1,
 225                   );
 226
 227 has 'file_metadata' => (isa => 'Str', is => 'rw', predicate => 'has_file_metadata');
 228 has 'trial_stock_type' => (isa => 'Str', is => 'rw', predicate => 'has_trial_stock_type', required => 0);
 229
 230 sub BUILD {
 231     my $self = shift;
 232     $self->load_plugin($self->format());
 233 }
 234
 235 # sub verify {
 236 #     my $self = shift;
 237
 238 #     $self->load_plugin($self->format());
 239
 240 #     return $self->plugin_verify();
 241 # }
 242
 243 # sub download {
 244 #     my $self = shift;
 245
 246 #     print STDERR "Format: ".$self->format()."\n";
 247 #     eval {
 248 #       $self->load_plugin($self->format());
 249 #     };
 250 #     if ($@) {
 251 #       die "The plugin specified (".$self->format().") for the download does not exist";
 252 #     }
 253
 254 #     my $error = $self->plugin_download();
 255
 256 #     return $error;
 257 # }
 258
 259 sub trial_download_log {
 260     my $self = shift;
 261     my $trial_id = shift;
 262     my $message = shift;
 263
 264     if (! $self->user_id && !$self->trial_download_logfile()) {
 265         return;
 266     }
 267     else {
 268         print STDERR "Note: set config variable trial_download_logfile to obtain a log of downloaded trials.\n";
 269     }
 270
 271     my $now = DateTime->now();
 272
 273     open (my $F, ">>", $self->trial_download_logfile()) || die "Can't open ".$self->trial_download_logfile();
 274     my $username = CXGN::People::Person->new($self->bcs_schema->storage->dbh(), $self->user_id())->get_username();
 275     print $F join("\t", (
 276                       $username,
 277                       $trial_id,
 278                       $message,
 279                       $now->year()."-".$now->month()."-".$now->day()." ".$now->hour().":".$now->minute()));
 280     print $F "\n";
 281
 282     close($F);
 283
 284
 285 }
 286
 287
 288 1;