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 use CXGN::List::Transform;
  15 use CXGN::List::Validate;
  16 use CXGN::List;
  17 use JSON;
  18
  19 BEGIN { extends 'Catalyst::Controller'; }
  20
  21
  22 sub trial_init : Chained('/') PathPart('breeders/trial') CaptureArgs(1) {
  23     my $self = shift;
  24     my $c = shift;
  25     my $trial_id = shift;
  26
  27     $c->stash->{trial_id} = $trial_id;
  28     print STDERR "TRIAL ID = $trial_id\n";
  29
  30     my $schema = $c->dbic_schema("Bio::Chado::Schema");
  31     $c->stash->{schema} = $schema;
  32     my $trial;
  33     eval {
  34         $trial = CXGN::Trial->new( { bcs_schema => $schema, trial_id => $trial_id });
  35     };
  36     if ($@) {
  37         $c->stash->{template} = 'system_message.txt';
  38         $c->stash->{message} = "The requested trial ($trial_id) does not exist";
  39         return;
  40     }
  41     $c->stash->{trial} = $trial;
  42 }
  43
  44 sub old_trial_url : Path('/breeders_toolbox/trial') Args(1) {
  45     my $self = shift;
  46     my $c = shift;
  47     my @args = @_;
  48     my $format = $c->req->param("format");
  49     $c->res->redirect('/breeders/trial/'.$args[0].'?format='.$format);
  50 }
  51
  52 sub trial_info : Chained('trial_init') PathPart('') Args(0) {
  53     #print STDERR "Check 1: ".localtime()."\n";
  54     print STDERR "TRIAL INIT...\n\n";
  55     my $self = shift;
  56     my $c = shift;
  57     my $format = $c->req->param("format");
  58     #print STDERR $format;
  59     my $user = $c->user();
  60     if (!$user) {
  61         $c->res->redirect( uri( path => '/solpeople/login.pl', query => { goto_url => $c->req->uri->path_query } ) );
  62         return;
  63     }
  64
  65     $c->stash->{user_can_modify} = ($user->check_roles("submitter") || $user->check_roles("curator")) ;
  66
  67     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
  68     my $trial = $c->stash->{trial};
  69     my $program_object = CXGN::BreedersToolbox::Projects->new( { schema => $schema });
  70
  71     if (!$program_object->trial_exists($c->stash->{trial_id})) {
  72         $c->stash->{message} = "The requested trial does not exist or has been deleted.";
  73         $c->stash->{template} = 'generic_message.mas';
  74         return;
  75     }
  76
  77     $c->stash->{trial_name} = $trial->get_name();
  78
  79     my $trial_type_data = $trial->get_project_type();
  80     $c->stash->{trial_type} = $trial_type_data->[1];
  81     $c->stash->{trial_type_id} = $trial_type_data->[0];
  82
  83     $c->stash->{planting_date} = $trial->get_planting_date();
  84
  85     $c->stash->{harvest_date} = $trial->get_harvest_date();
  86
  87     $c->stash->{trial_description} = $trial->get_description();
  88     $c->stash->{trial_phenotype_files} = $trial->get_phenotype_metadata();
  89     $c->stash->{assayed_traits} = $trial->get_traits_assayed();
  90
  91     my $location_data = $trial->get_location();
  92     $c->stash->{location_id} = $location_data->[0];
  93     $c->stash->{location_name} = $location_data->[1];
  94
  95     my $breeding_program_data = $program_object->get_breeding_programs_by_trial($c->stash->{trial_id});
  96     $c->stash->{breeding_program_id} = $breeding_program_data->[0]->[0];
  97     $c->stash->{breeding_program_name} = $breeding_program_data->[0]->[1];
  98
  99     $c->stash->{year} = $trial->get_year();
 100
 101     $c->stash->{trial_id} = $c->stash->{trial_id};
 102
 103     $c->stash->{has_col_and_row_numbers} = $trial->has_col_and_row_numbers();
 104     $c->stash->{has_plant_entries} = $trial->has_plant_entries();
 105     $c->stash->{has_subplot_entries} = $trial->has_subplot_entries();
 106     $c->stash->{has_tissue_sample_entries} = $trial->has_tissue_sample_entries();
 107     $c->stash->{phenotypes_fully_uploaded} = $trial->get_phenotypes_fully_uploaded();
 108
 109     $c->stash->{hidap_enabled} = $c->config->{hidap_enabled};
 110     $c->stash->{has_expression_atlas} = $c->config->{has_expression_atlas};
 111     $c->stash->{expression_atlas_url} = $c->config->{expression_atlas_url};
 112     $c->stash->{main_production_site_url} = $c->config->{main_production_site_url};
 113     $c->stash->{site_project_name} = $c->config->{project_name};
 114     $c->stash->{sgn_session_id} = $c->req->cookie('sgn_session_id');
 115     $c->stash->{user_name} = $c->user->get_object->get_username;
 116
 117     if ($trial->get_folder) {
 118       $c->stash->{folder_id} = $trial->get_folder()->project_id();
 119       $c->stash->{folder_name} = $trial->get_folder()->name();
 120     }
 121
 122     my $design_type = $trial->get_design_type();
 123     $c->stash->{design_name} = $design_type;
 124
 125     #  print STDERR "TRIAL TYPE DATA = $trial_type_data->[1]\n\n";
 126
 127     if ($design_type eq "genotyping_plate") {
 128         $c->stash->{plate_id} = $c->stash->{trial_id};
 129         $c->stash->{genotyping_facility} = $trial->get_genotyping_facility;
 130         $c->stash->{genotyping_facility_submitted} = $trial->get_genotyping_facility_submitted;
 131         $c->stash->{genotyping_facility_status} = $trial->get_genotyping_facility_status;
 132         $c->stash->{genotyping_plate_sample_type} = $trial->get_genotyping_plate_sample_type;
 133         if ($trial->get_genotyping_plate_format){
 134             $c->stash->{genotyping_plate_format} = $trial->get_genotyping_plate_format;
 135         }
 136         if ($format eq "as_table") {
 137             $c->stash->{template} = '/breeders_toolbox/genotyping_trials/format/as_table.mas';
 138         }
 139         else {
 140             $c->stash->{template} = '/breeders_toolbox/genotyping_trials/detail.mas';
 141         }
 142     }
 143     elsif ($design_type eq "treatment"){
 144         $c->stash->{template} = '/breeders_toolbox/treatment.mas';
 145     }
 146     else {
 147         $c->stash->{template} = '/breeders_toolbox/trial.mas';
 148     }
 149
 150     if ($trial_type_data->[1] eq "crossing_trial"){
 151         print STDERR "It's a crossing trial!\n\n";
 152         $c->stash->{template} = '/breeders_toolbox//cross/crossing_trial.mas';
 153     }
 154
 155     print STDERR "End Load Trial Detail Page: ".localtime()."\n";
 156
 157 }
 158
 159
 160 sub trait_info :Path('/breeders/trial') Args(3) {
 161     my ($self, $c, $trial_id, $trait_txt, $trait_id) = @_;
 162
 163     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 164
 165     my $trial_name = $schema->resultset("Project::Project")
 166         ->search( {'me.project_id' => $trial_id})
 167         ->single
 168         ->name;
 169
 170     $c->stash->{trial_name} = $trial_name;
 171
 172     my $trait_name = $schema->resultset("Cv::Cvterm")
 173         ->search({'me.cvterm_id' => $trait_id})
 174         ->single
 175         ->name;
 176
 177     $c->stash->{trial_id}   = $trial_id;
 178     $c->stash->{trial_name} = $trial_name;
 179
 180     $c->stash->{trait_id}   = $trait_id;
 181     $c->stash->{trait_name} = $trait_name;
 182
 183     $c->stash->{template}   = '/breeders_toolbox/trial_trait.mas';
 184 }
 185
 186 ##DEPRECATED by /breeders/trials
 187 sub trial_tree : Path('/breeders/trialtree') Args(0) {
 188     my $self = shift;
 189     my $c = shift;
 190
 191
 192     $c->stash->{template} = '/breeders_toolbox/trialtree.mas';
 193
 194 }
 195
 196 #For downloading trial layout in CSV and Excel, for downloading trial phenotypes in CSV and Excel, and for downloading trial phenotyping spreadsheets in Excel.
 197 #For phenotype download, better to use SGN::Controller::BreedersToolbox::Download->download_phenotypes_action and provide a single trial_id in the trial_list argument, as that is how the phenotype download works from the wizard page, the trial tree page, and the trial detail page for phenotype download.
 198 sub trial_download : Chained('trial_init') PathPart('download') Args(1) {
 199     my $self = shift;
 200     my $c = shift;
 201     my $what = shift;
 202     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 203
 204     my $user = $c->user();
 205     if (!$user) {
 206         $c->res->redirect( uri( path => '/solpeople/login.pl', query => { goto_url => $c->req->uri->path_query } ) );
 207         return;
 208     }
 209
 210     my $format = $c->req->param("format") || "xls";
 211     my $data_level = $c->req->param("dataLevel") || "plot";
 212     my $timestamp_option = $c->req->param("timestamp") || 0;
 213     my $trait_list = $c->req->param("trait_list");
 214     my $search_type = $c->req->param("search_type") || 'fast';
 215
 216     my $trial = $c->stash->{trial};
 217     if ($data_level eq 'plants') {
 218         if (!$trial->has_plant_entries()) {
 219             $c->stash->{template} = 'generic_message.mas';
 220             $c->stash->{message} = "The requested trial (".$trial->get_name().") does not have plant entries. Please create the plant entries first.";
 221             return;
 222         }
 223     }
 224     if ($data_level eq 'subplots' || $data_level eq 'plants_subplots') {
 225         if (!$trial->has_subplot_entries()) {
 226             $c->stash->{template} = 'generic_message.mas';
 227             $c->stash->{message} = "The requested trial (".$trial->get_name().") does not have subplot entries.";
 228             return;
 229         }
 230     }
 231
 232     my $selected_cols = $c->req->param('selected_columns') ? decode_json $c->req->param('selected_columns') : {};
 233     if ($data_level eq 'plate'){
 234         $selected_cols = {'trial_name'=>1, 'acquisition_date'=>1, 'plot_name'=>1, 'plot_number'=>1, 'row_number'=>1, 'col_number'=>1, 'source_observation_unit_name'=>1, 'accession_name'=>1, 'dna_person'=>1, 'notes'=>1, 'tissue_type'=>1, 'extraction'=>1, 'concentration'=>1, 'volume'=>1, 'is_blank'=>1};
 235     }
 236     my $selected_trait_list_id = $c->req->param('trait_list_id');
 237     my @selected_trait_names;
 238     my @trait_list;
 239     if ($selected_trait_list_id){
 240         my $list = CXGN::List->new({ dbh => $c->dbc->dbh, list_id => $selected_trait_list_id });
 241         @selected_trait_names = @{$list->elements()};
 242         my $validator = CXGN::List::Validate->new();
 243         my @absent_traits = @{$validator->validate($schema, 'traits', \@selected_trait_names)->{'missing'}};
 244         if (scalar(@absent_traits)>0){
 245             $c->stash->{template} = 'generic_message.mas';
 246             $c->stash->{message} = "Trait list is not valid because of these terms: ".join ',',@absent_traits;
 247             return;
 248         }
 249         my $lt = CXGN::List::Transform->new();
 250         @trait_list = @{$lt->transform($schema, "traits_2_trait_ids", \@selected_trait_names)->{transform}};
 251     }
 252
 253     my @treatment_project_ids;
 254     my $treatments = $trial->get_treatments();
 255     foreach (@$treatments){
 256         push @treatment_project_ids, $_->[0];
 257     }
 258
 259     if ($trait_list && $trait_list ne 'null') {
 260         @trait_list = @{_parse_list_from_json($trait_list)};
 261     }
 262
 263     my $plugin = "";
 264     if ( ($format eq "xls") && ($what eq "layout")) {
 265         $plugin = "TrialLayoutExcel";
 266     }
 267     if (($format eq "csv") && ($what eq "layout")) {
 268         $plugin = "TrialLayoutCSV";
 269     }
 270     if (($format eq "xls") && ($what =~ /phenotype/)) {
 271         $plugin = "TrialPhenotypeExcel";
 272     }
 273     if (($format eq "csv") && ($what =~ /phenotype/)) {
 274         $plugin = "TrialPhenotypeCSV";
 275     }
 276     if (($format eq "xls") && ($what eq "basic_trial_excel")) {
 277         $plugin = "BasicExcel";
 278     }
 279     if ( ($format eq "intertekxls") && ($what eq "layout")) {
 280         $plugin = "GenotypingTrialLayoutIntertekXLS";
 281     }
 282
 283     my $trial_name = $trial->get_name();
 284     my $trial_id = $trial->get_trial_id();
 285     my $dir = $c->tempfiles_subdir('download');
 286     my $temp_file_name = $trial_id . "_" . "$what" . "XXXX";
 287     my $rel_file = $c->tempfile( TEMPLATE => "download/$temp_file_name");
 288     $rel_file = $rel_file . ".$format";
 289     my $tempfile = $c->config->{basepath}."/".$rel_file;
 290
 291     print STDERR "TEMPFILE : $tempfile\n";
 292
 293     my $download = CXGN::Trial::Download->new({
 294         bcs_schema => $schema,
 295         trial_id => $c->stash->{trial_id},
 296         trait_list => \@trait_list,
 297         filename => $tempfile,
 298         format => $plugin,
 299         data_level => $data_level,
 300         search_type => $search_type,
 301         include_timestamp => $timestamp_option,
 302         treatment_project_ids => \@treatment_project_ids,
 303         selected_columns => $selected_cols,
 304         selected_trait_names => \@selected_trait_names,
 305     });
 306
 307     my $error = $download->download();
 308
 309     if ($format eq 'intertekxls'){
 310         $format = 'xls';
 311     }
 312
 313     my $file_name = $trial_id . "_" . "$what" . ".$format";
 314     $c->res->content_type('Application/'.$format);
 315     $c->res->header('Content-Disposition', qq[attachment; filename="$file_name"]);
 316
 317     my $output = read_file($tempfile);
 318
 319     $c->res->body($output);
 320
 321 }
 322
 323 sub _parse_list_from_json {
 324     my $list_json = shift;
 325     my $json = new JSON;
 326     if ($list_json) {
 327         my $decoded_list = $json->allow_nonref->utf8->relaxed->escape_slash->loose->allow_singlequote->allow_barekey->decode($list_json);
 328         #my $decoded_list = decode_json($list_json);
 329         my @array_of_list_items = @{$decoded_list};
 330         return \@array_of_list_items;
 331     }
 332     else {
 333         return;
 334     }
 335 }
 336
 337
 338 1;