lib/SGN/Controller/BreedersToolbox/Trial.pm

   1
   2 package SGN::Controller::BreedersToolbox::Trial;
   3
   4 use Moose;
   5
   6 use File::Basename;
   7 use File::Slurp qw | read_file |;
   8 use URI::FromHash 'uri';
   9
  10 use CXGN::Trial::TrialLayout;
  11 use CXGN::BreedersToolbox::Projects;
  12 use SGN::View::Trial qw/design_layout_view design_info_view trial_detail_design_view/;
  13 use CXGN::Trial::Download;
  14
  15 BEGIN { extends 'Catalyst::Controller'; }
  16
  17
  18 sub trial_init : Chained('/') PathPart('breeders/trial') CaptureArgs(1) {
  19     my $self = shift;
  20     my $c = shift;
  21     my $trial_id = shift;
  22
  23     $c->stash->{trial_id} = $trial_id;
  24     print STDERR "TRIAL ID = $trial_id\n";
  25
  26     my $schema = $c->dbic_schema("Bio::Chado::Schema");
  27     $c->stash->{schema} = $schema;
  28     my $trial;
  29     eval {
  30         $trial = CXGN::Trial->new( { bcs_schema => $schema, trial_id => $trial_id });
  31     };
  32     if ($@) {
  33         $c->stash->{template} = 'system_message.txt';
  34         $c->stash->{message} = "The requested trial ($trial_id) does not exist";
  35         return;
  36     }
  37     $c->stash->{trial} = $trial;
  38 }
  39
  40 sub old_trial_url : Path('/breeders_toolbox/trial') Args(1) {
  41     my $self = shift;
  42     my $c = shift;
  43     my @args = @_;
  44     my $format = $c->req->param("format");
  45     $c->res->redirect('/breeders/trial/'.$args[0].'?format='.$format);
  46 }
  47
  48 sub trial_info : Chained('trial_init') PathPart('') Args(0) {
  49     #print STDERR "Check 1: ".localtime()."\n";
  50     my $self = shift;
  51     my $c = shift;
  52     my $format = $c->req->param("format");
  53     #print STDERR $format;
  54     my $user = $c->user();
  55     if (!$user) {
  56         $c->res->redirect( uri( path => '/solpeople/login.pl', query => { goto_url => $c->req->uri->path_query } ) );
  57         return;
  58     }
  59
  60     $c->stash->{user_can_modify} = ($user->check_roles("submitter") || $user->check_roles("curator")) ;
  61
  62     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
  63     my $trial = $c->stash->{trial};
  64     my $program_object = CXGN::BreedersToolbox::Projects->new( { schema => $schema });
  65
  66     if (!$program_object->trial_exists($c->stash->{trial_id})) {
  67         $c->stash->{message} = "The requested trial does not exist or has been deleted.";
  68         $c->stash->{template} = 'generic_message.mas';
  69         return;
  70     }
  71
  72     $c->stash->{trial_name} = $trial->get_name();
  73
  74     my $trial_type_data = $trial->get_project_type();
  75     $c->stash->{trial_type} = $trial_type_data->[1];
  76
  77     $c->stash->{planting_date} = $trial->get_planting_date();
  78
  79     $c->stash->{harvest_date} = $trial->get_harvest_date();
  80
  81     $c->stash->{trial_description} = $trial->get_description();
  82
  83     my $location_data = $trial->get_location();
  84     $c->stash->{location_id} = $location_data->[0];
  85     $c->stash->{location_name} = $location_data->[1];
  86
  87     my $breeding_program_data = $program_object->get_breeding_programs_by_trial($c->stash->{trial_id});
  88     $c->stash->{breeding_program_id} = $breeding_program_data->[0]->[0];
  89     $c->stash->{breeding_program_name} = $breeding_program_data->[0]->[1];
  90
  91     $c->stash->{year} = $trial->get_year();
  92
  93     $c->stash->{trial_id} = $c->stash->{trial_id};
  94
  95     $c->stash->{has_plant_entries} = $trial->has_plant_entries();
  96
  97     $c->stash->{hidap_enabled} = $c->config->{hidap_enabled};
  98
  99     if ($trial->get_folder) {
 100       $c->stash->{folder_id} = $trial->get_folder()->project_id();
 101       $c->stash->{folder_name} = $trial->get_folder()->name();
 102     }
 103
 104     my $design_type = $trial->get_design_type();
 105
 106     if ($design_type eq "genotyping_plate") {
 107         if ($format eq "as_table") {
 108             $c->stash->{template} = '/breeders_toolbox/genotyping_trials/format/as_table.mas';
 109         }
 110         else {
 111             $c->stash->{template} = '/breeders_toolbox/genotyping_trials/detail.mas';
 112         }
 113
 114     }
 115     else {
 116         $c->stash->{template} = '/breeders_toolbox/trial.mas';
 117     }
 118
 119     print STDERR "End Load Trial Detail Page: ".localtime()."\n";
 120
 121 }
 122
 123
 124 sub trait_info :Path('/breeders/trial') Args(3) {
 125     my ($self, $c, $trial_id, $trait_txt, $trait_id) = @_;
 126
 127     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 128
 129     my $trial_name = $schema->resultset("Project::Project")
 130         ->search( {'me.project_id' => $trial_id})
 131         ->single
 132         ->name;
 133
 134     $c->stash->{trial_name} = $trial_name;
 135
 136     my $trait_name = $schema->resultset("Cv::Cvterm")
 137         ->search({'me.cvterm_id' => $trait_id})
 138         ->single
 139         ->name;
 140
 141     $c->stash->{trial_id}   = $trial_id;
 142     $c->stash->{trial_name} = $trial_name;
 143
 144     $c->stash->{trait_id}   = $trait_id;
 145     $c->stash->{trait_name} = $trait_name;
 146
 147     $c->stash->{template}   = '/breeders_toolbox/trial_trait.mas';
 148 }
 149
 150
 151 sub trial_tree : Path('/breeders/trialtree') Args(0) {
 152     my $self = shift;
 153     my $c = shift;
 154
 155
 156     $c->stash->{template} = '/breeders_toolbox/trialtree.mas';
 157
 158 }
 159
 160 sub trial_download : Chained('trial_init') PathPart('download') Args(1) {
 161     my $self = shift;
 162     my $c = shift;
 163     my $what = shift;
 164
 165
 166     my $user = $c->user();
 167     if (!$user) {
 168         $c->res->redirect( uri( path => '/solpeople/login.pl', query => { goto_url => $c->req->uri->path_query } ) );
 169         return;
 170     }
 171
 172     my $format = $c->req->param("format") || "xls";
 173     my $data_level = $c->req->param("dataLevel") || "plots";
 174     my $timestamp_option = $c->req->param("timestamp") || 0;
 175     my $trait_list = $c->req->param("trait_list") || "";
 176
 177     if ($data_level eq 'plants') {
 178         my $trial = $c->stash->{trial};
 179         if (!$trial->has_plant_entries()) {
 180             $c->stash->{template} = 'generic_message.mas';
 181             $c->stash->{message} = "The requested trial (".$trial->get_name().") does not have plant entries. Please create the plant entries first.";
 182             return;
 183         }
 184     }
 185
 186     my @trait_list;
 187     if ($trait_list) {
 188         @trait_list = @{_parse_list_from_json($trait_list)};
 189     }
 190
 191     my $plugin = "";
 192     if ( ($format eq "xls") && ($what eq "layout")) {
 193         $plugin = "TrialLayoutExcel";
 194     }
 195     if (($format eq "csv") && ($what eq "layout")) {
 196         $plugin = "TrialLayoutCSV";
 197     }
 198     if (($format eq "xls") && ($what =~ /phenotype/)) {
 199         $plugin = "TrialPhenotypeExcel";
 200     }
 201     if (($format eq "csv") && ($what =~ /phenotype/)) {
 202         $plugin = "TrialPhenotypeCSV";
 203     }
 204     if (($format eq "xls") && ($what eq "basic_trial_excel")) {
 205         $plugin = "BasicExcel";
 206     }
 207
 208     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 209     my $trial = CXGN::Trial->new({bcs_schema => $schema, trial_id => $c->stash->{trial_id} });
 210     my $trial_name = $trial->get_name();
 211     my $trial_id = $trial->get_trial_id();
 212     my $dir = $c->tempfiles_subdir('download');
 213     my $temp_file_name = $trial_id . "_" . "$what" . "XXXX";
 214     my $rel_file = $c->tempfile( TEMPLATE => "download/$temp_file_name");
 215     $rel_file = $rel_file . ".$format";
 216     my $tempfile = $c->config->{basepath}."/".$rel_file;
 217
 218     print STDERR "TEMPFILE : $tempfile\n";
 219
 220     my $download = CXGN::Trial::Download->new(
 221         {
 222             bcs_schema => $c->stash->{schema},
 223             trial_id => $c->stash->{trial_id},
 224             trait_list => \@trait_list,
 225             filename => $tempfile,
 226             format => $plugin,
 227         data_level => $data_level,
 228         include_timestamp => $timestamp_option,
 229       });
 230
 231       my $error = $download->download();
 232
 233       my $file_name = $trial_id . "_" . "$what" . ".$format";
 234      $c->res->content_type('Application/'.$format);
 235      $c->res->header('Content-Disposition', qq[attachment; filename="$file_name"]);
 236
 237     my $output = read_file($tempfile);
 238
 239     $c->res->body($output);
 240
 241 }
 242
 243 sub _parse_list_from_json {
 244     my $list_json = shift;
 245     my $json = new JSON;
 246     if ($list_json) {
 247         my $decoded_list = $json->allow_nonref->utf8->relaxed->escape_slash->loose->allow_singlequote->allow_barekey->decode($list_json);
 248         #my $decoded_list = decode_json($list_json);
 249         my @array_of_list_items = @{$decoded_list};
 250         return \@array_of_list_items;
 251     }
 252     else {
 253         return;
 254     }
 255 }
 256
 257
 258 1;