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::XS;
  18 use Data::Dumper;
  19 use CXGN::TrialStatus;
  20 use SGN::Model::Cvterm;
  21 use CXGN::Genotype::GenotypingProject;
  22 use CXGN::Stock::TissueSample::Search;
  23 use CXGN::Genotype::Protocol;
  24 use CXGN::TrackingActivity::ActivityProject;
  25 use CXGN::Transformation::Transformation;
  26
  27 BEGIN { extends 'Catalyst::Controller'; }
  28
  29
  30 sub trial_init : Chained('/') PathPart('breeders/trial') CaptureArgs(1) {
  31     my $self = shift;
  32     my $c = shift;
  33     my $trial_id = shift;
  34
  35     $c->stash->{trial_id} = $trial_id;
  36 #    print STDERR "TRIAL ID = $trial_id\n";
  37
  38     my $schema = $c->dbic_schema("Bio::Chado::Schema");
  39     $c->stash->{schema} = $schema;
  40     my $trial;
  41     eval {
  42         $trial = CXGN::Trial->new( { bcs_schema => $schema, trial_id => $trial_id });
  43     };
  44     if ($@) {
  45         $c->stash->{template} = 'system_message.txt';
  46         $c->stash->{message} = "The requested trial ($trial_id) does not exist";
  47         return;
  48     }
  49     $c->stash->{trial} = $trial;
  50 }
  51
  52 sub old_trial_url : Path('/breeders_toolbox/trial') Args(1) {
  53     my $self = shift;
  54     my $c = shift;
  55     my @args = @_;
  56     my $format = $c->req->param("format");
  57     $c->res->redirect('/breeders/trial/'.$args[0].'?format='.$format);
  58 }
  59
  60 sub trial_info : Chained('trial_init') PathPart('') Args(0) {
  61     #print STDERR "Check 1: ".localtime()."\n";
  62     #print STDERR "TRIAL INIT...\n\n";
  63     my $self = shift;
  64     my $c = shift;
  65     my $format = $c->req->param("format");
  66     #print STDERR $format;
  67     my $user = $c->user();
  68     if (!$user) {
  69         $c->res->redirect( uri( path => '/user/login', query => { goto_url => $c->req->uri->path_query } ) );
  70         return;
  71     }
  72
  73     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
  74     my $trial = $c->stash->{trial};
  75     my $program_object = CXGN::BreedersToolbox::Projects->new( { schema => $schema });
  76
  77     if (!$program_object->trial_exists($c->stash->{trial_id})) {
  78         $c->stash->{message} = "The requested trial does not exist or has been deleted.";
  79         $c->stash->{template} = 'generic_message.mas';
  80         return;
  81     }
  82
  83     $c->stash->{trial_name} = $trial->get_name();
  84     $c->stash->{trial_owner} = $trial->get_owner_link();
  85
  86     my $trial_type_data = $trial->get_project_type();
  87     my $trial_type_name = $trial_type_data ? $trial_type_data->[1] : '';
  88     $c->stash->{trial_type} = $trial_type_name;
  89     $c->stash->{trial_type_id} = $trial_type_data->[0];
  90
  91     $c->stash->{planting_date} = $trial->get_planting_date();
  92     $c->stash->{show_transplanting_date} = $c->config->{show_transplanting_date};
  93     $c->stash->{transplanting_date} = $trial->get_transplanting_date();
  94     warn "Transplanting Date: ".$c->stash->{transplanting_date};
  95     $c->stash->{harvest_date} = $trial->get_harvest_date();
  96
  97     $c->stash->{plot_width} = $trial->get_plot_width();
  98     $c->stash->{plot_length} = $trial->get_plot_length();
  99     $c->stash->{field_size} = $trial->get_field_size();
 100
 101     $c->stash->{field_trial_is_planned_to_be_genotyped} = $trial->get_field_trial_is_planned_to_be_genotyped();
 102     $c->stash->{field_trial_is_planned_to_cross} = $trial->get_field_trial_is_planned_to_cross();
 103
 104     $c->stash->{trial_description} = $trial->get_description();
 105
 106     my $activities = $c->config->{'trial_activities'};
 107     my @activity_list = split ',', $activities;
 108     my $trial_status = CXGN::TrialStatus->new({ bcs_schema => $schema, parent_id => $c->stash->{trial_id}, activity_list => \@activity_list });
 109     $c->stash->{latest_trial_activity} = $trial_status->get_latest_activity();
 110
 111     my $location_data = $trial->get_location();
 112     $c->stash->{location_id} = $location_data->[0];
 113     $c->stash->{location_name} = $location_data->[1];
 114     $c->stash->{country_name} = $trial->get_location_country_name();
 115
 116     my $breeding_program_data = $program_object->get_breeding_programs_by_trial($c->stash->{trial_id});
 117     $c->stash->{breeding_program_id} = $breeding_program_data->[0]->[0];
 118     $c->stash->{breeding_program_name} = $breeding_program_data->[0]->[1];
 119
 120     $c->stash->{user_can_modify} = ($user->check_roles("submitter") && $user->check_roles($c->stash->{breeding_program_name})) || $user->check_roles("curator") ;
 121
 122
 123
 124     $c->stash->{year} = $trial->get_year();
 125
 126     $c->stash->{trial_id} = $c->stash->{trial_id};
 127
 128     $c->stash->{has_col_and_row_numbers} = $trial->has_col_and_row_numbers();
 129     $c->stash->{has_plant_entries} = $trial->has_plant_entries();
 130     $c->stash->{has_subplot_entries} = $trial->has_subplot_entries();
 131     $c->stash->{has_tissue_sample_entries} = $trial->has_tissue_sample_entries();
 132     $c->stash->{phenotypes_fully_uploaded} = $trial->get_phenotypes_fully_uploaded();
 133
 134     $c->stash->{hidap_enabled} = $c->config->{hidap_enabled};
 135     $c->stash->{has_expression_atlas} = $c->config->{has_expression_atlas};
 136     $c->stash->{expression_atlas_url} = $c->config->{expression_atlas_url};
 137     $c->stash->{main_production_site_url} = $c->config->{main_production_site_url};
 138     $c->stash->{site_project_name} = $c->config->{project_name};
 139     $c->stash->{sgn_session_id} = $c->req->cookie('sgn_session_id');
 140     $c->stash->{user_name} = $c->user->get_object->get_username;
 141
 142     if ($trial->get_folder) {
 143       $c->stash->{folder_id} = $trial->get_folder()->project_id();
 144       $c->stash->{folder_name} = $trial->get_folder()->name();
 145     }
 146
 147     my $design_type = $trial->get_design_type();
 148     $c->stash->{design_name} = $design_type;
 149     $c->stash->{genotyping_facility} = $trial->get_genotyping_facility;
 150
 151     my $activity_project = CXGN::TrackingActivity::ActivityProject->new( { bcs_schema => $schema, trial_id => $c->stash->{trial_id} });
 152
 153     #  print STDERR "TRIAL TYPE DATA = $trial_type_data->[1]\n\n";
 154
 155     if ($design_type eq "genotyping_plate") {
 156         my $plate_id = $c->stash->{trial_id};
 157         $c->stash->{plate_id} = $plate_id;
 158         $c->stash->{raw_data_link} = $trial->get_raw_data_link;
 159         $c->stash->{genotyping_facility} = $trial->get_genotyping_facility;
 160         $c->stash->{genotyping_facility_submitted} = $trial->get_genotyping_facility_submitted;
 161         $c->stash->{genotyping_facility_status} = $trial->get_genotyping_facility_status;
 162         $c->stash->{genotyping_vendor_order_id} = $trial->get_genotyping_vendor_order_id;
 163         $c->stash->{genotyping_vendor_submission_id} = $trial->get_genotyping_vendor_submission_id;
 164         $c->stash->{genotyping_plate_sample_type} = $trial->get_genotyping_plate_sample_type;
 165
 166         my $sample_data_search = CXGN::Stock::TissueSample::Search->new({
 167             bcs_schema=>$schema,
 168             plate_db_id_list => [$plate_id],
 169         });
 170
 171         my $data = $sample_data_search->get_sample_data();
 172         $c->stash->{number_of_samples} = $data->{number_of_samples};
 173         $c->stash->{number_of_samples_with_data} = $data->{number_of_samples_with_data};
 174
 175         my $genotyping_project_relationship_cvterm = SGN::Model::Cvterm->get_cvterm_row($schema, 'genotyping_project_and_plate_relationship', 'project_relationship');
 176         my $genotyping_project_plate_relationship = $schema->resultset("Project::ProjectRelationship")->find ({
 177             subject_project_id => $plate_id,
 178             type_id => $genotyping_project_relationship_cvterm->cvterm_id()
 179         });
 180         if ($genotyping_project_plate_relationship) {
 181             my $genotyping_project_id = $genotyping_project_plate_relationship->object_project_id();
 182             my $genotyping_project = $schema->resultset("Project::Project")->find ({
 183                 project_id => $genotyping_project_id
 184             });
 185             my $genotyping_project_name = $genotyping_project->name();
 186             my $genotyping_project_link = '<a href="/breeders/trial/'.$genotyping_project_id.'">'.$genotyping_project_name.'</a>';
 187             $c->stash->{genotyping_project_link} = $genotyping_project_link;
 188         }
 189
 190         if ($trial->get_genotyping_plate_format){
 191             $c->stash->{genotyping_plate_format} = $trial->get_genotyping_plate_format;
 192         }
 193         if ($format eq "as_table") {
 194             $c->stash->{template} = '/breeders_toolbox/genotyping_trials/format/as_table.mas';
 195         }
 196         else {
 197             $c->stash->{template} = '/breeders_toolbox/genotyping_trials/detail.mas';
 198         }
 199     }
 200     elsif ($design_type eq "sampling_trial"){
 201         $c->stash->{template} = '/breeders_toolbox/sampling_trials/detail.mas';
 202     }
 203     elsif ($design_type eq "treatment"){
 204         $c->stash->{management_factor_type} = $trial->get_management_factor_type;
 205         $c->stash->{management_factor_date} = $trial->get_management_factor_date;
 206         $c->stash->{template} = '/breeders_toolbox/management_factor.mas';
 207     }
 208     elsif (($design_type eq "genotype_data_project") || ($design_type eq "pcr_genotype_data_project")){
 209         my $project_id = $c->stash->{trial_id};
 210         if ($design_type eq "pcr_genotype_data_project") {
 211             $c->stash->{genotype_data_type} = 'SSR'
 212         } else {
 213             $c->stash->{genotype_data_type} = 'SNP'
 214         }
 215
 216         my $project_info = CXGN::Genotype::GenotypingProject->new({
 217             bcs_schema => $schema,
 218             project_id => $project_id
 219         });
 220         my ($data, $tc) = $project_info->get_plate_info();
 221         my $has_plate;
 222         if (!$data) {
 223             $has_plate = 'none';
 224         }
 225         $c->stash->{has_plate} = $has_plate;
 226
 227         my $associated_protocol  = $project_info->get_associated_protocol();
 228
 229         if ( defined $associated_protocol && scalar(@$associated_protocol)>0) {
 230             my $protocol_id = $associated_protocol->[0]->[0];
 231             my $protocol_info = CXGN::Genotype::Protocol->new({
 232                 bcs_schema => $schema,
 233                 nd_protocol_id => $protocol_id
 234             });
 235
 236             my $marker_names = $protocol_info->{marker_names};
 237             my $assay_type = $protocol_info->{assay_type};
 238             $c->stash->{marker_names} = $marker_names;
 239             $c->stash->{assay_type} = $assay_type;
 240
 241             my $marker_info_keys = $protocol_info->marker_info_keys;
 242             my @marker_info_headers = ();
 243             if (defined $marker_info_keys) {
 244                 foreach my $info_key (@$marker_info_keys) {
 245                     if ($info_key eq 'name') {
 246                         push @marker_info_headers, 'Marker Name';
 247                     } elsif (($info_key eq 'intertek_name') || ($info_key eq 'facility_name')) {
 248                         push @marker_info_headers, 'Facility Marker Name';
 249                     } elsif ($info_key eq 'chrom') {
 250                         push @marker_info_headers, 'Chromosome';
 251                     } elsif ($info_key eq 'pos') {
 252                         push @marker_info_headers, 'Position';
 253                     } elsif ($info_key eq 'alt') {
 254                         if ($assay_type eq 'KASP') {
 255                             push @marker_info_headers, 'Y-allele';
 256                         } else {
 257                             push @marker_info_headers, 'Alternate';
 258                         }
 259                     } elsif ($info_key eq 'ref') {
 260                         if ($assay_type eq 'KASP') {
 261                             push @marker_info_headers, 'X-allele';
 262                         } else {
 263                             push @marker_info_headers, 'Reference';
 264                         }
 265                     } elsif ($info_key eq 'qual') {
 266                         push @marker_info_headers, 'Quality';
 267                     } elsif ($info_key eq 'filter') {
 268                         push @marker_info_headers, 'Filter';
 269                     } elsif ($info_key eq 'info') {
 270                         push @marker_info_headers, 'Info';
 271                     } elsif ($info_key eq 'format') {
 272                         push @marker_info_headers, 'Format';
 273                     } elsif ($info_key eq 'sequence') {
 274                         push @marker_info_headers, 'Sequence';
 275                     }
 276                 }
 277             } else {
 278                 @marker_info_headers = ('Marker Name','Chromosome','Position','Alternate','Reference','Quality','Filter','Info','Format');
 279             }
 280             $c->stash->{marker_info_headers} = \@marker_info_headers;
 281         }
 282
 283         $c->stash->{template} = '/breeders_toolbox/genotype_data_project.mas';
 284     }
 285     elsif ($design_type eq "drone_run"){
 286         $c->stash->{drone_run_date} = $trial->get_drone_run_date;
 287         $c->stash->{template} = '/breeders_toolbox/drone_run_project.mas';
 288     }
 289     elsif ($trial_type_name eq "crossing_trial"){
 290         print STDERR "It's a crossing trial!\n\n";
 291         my $program_name = $breeding_program_data->[0]->[1];
 292         my $locations = $program_object->get_all_locations_by_breeding_program();
 293         my @locations_by_program;
 294         foreach my $location_hashref (@$locations) {
 295             my $properties = $location_hashref->{'properties'};
 296             my $program = $properties->{'Program'};
 297             my $name = $properties->{'Name'};
 298             if ($program eq $program_name) {
 299                 push @locations_by_program, $name;
 300             }
 301         }
 302         my $locations_by_program_json = encode_json(\@locations_by_program);
 303         $c->stash->{locations_by_program_json} = $locations_by_program_json;
 304         $c->stash->{template} = '/breeders_toolbox/cross/crossing_trial.mas';
 305     } elsif ($trial_type_name eq 'activity_record') {
 306         my $project_id = $c->stash->{trial_id};
 307         my $project_vendor_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'project_vendor', 'project_property')->cvterm_id();
 308         my $activity_type_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'activity_type', 'project_property')->cvterm_id();
 309
 310         my $activity_type = $schema->resultset("Project::Projectprop")->find ({ project_id => $project_id, type_id => $activity_type_cvterm_id })->value();
 311         $c->stash->{activity_type} = $activity_type;
 312
 313         my $input_field_headers;
 314         if ($activity_type eq 'tissue_culture') {
 315             $input_field_headers = $c->config->{tracking_tissue_culture_info_header};
 316         } elsif ($activity_type eq 'transformation') {
 317             $input_field_headers = $c->config->{tracking_transformation_info_header};
 318         }
 319         my @field_headers = split ',',$input_field_headers;
 320         $c->stash->{field_headers} = \@field_headers;
 321
 322         my $project_vendor_rs = $schema->resultset("Project::Projectprop")->find ({
 323             project_id => $project_id,
 324             type_id => $project_vendor_cvterm_id
 325         });
 326         my $vendor_id;
 327         if ($project_vendor_rs) {
 328             $vendor_id = $project_vendor_rs->value();
 329         }
 330
 331         $c->stash->{vendor_id} = $vendor_id;
 332
 333         my $progress_of_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema,'progress_of', 'project_relationship')->cvterm_id();
 334         my $project_rel_row = $schema->resultset('Project::ProjectRelationship')->find({subject_project_id => $project_id, type_id => $progress_of_cvterm_id });
 335         if ($project_rel_row) {
 336             my $parent_project_id = $project_rel_row->object_project_id;
 337             $c->stash->{parent_project_id} = $parent_project_id;
 338         }
 339
 340         $c->stash->{template} = '/tracking_activities/activity_project.mas';
 341     }
 342     elsif ($trial_type_name eq "transformation_project"){
 343         my $transformation_project_id = $c->stash->{trial_id};
 344         my $program_name = $breeding_program_data->[0]->[1];
 345         my $locations = $program_object->get_all_locations_by_breeding_program();
 346         my @locations_by_program;
 347         foreach my $location_hashref (@$locations) {
 348             my $properties = $location_hashref->{'properties'};
 349             my $program = $properties->{'Program'};
 350             my $name = $properties->{'Name'};
 351             if ($program eq $program_name) {
 352                 push @locations_by_program, $name;
 353             }
 354         }
 355         my $locations_by_program_json = encode_json(\@locations_by_program);
 356         $c->stash->{locations_by_program_json} = $locations_by_program_json;
 357
 358         my $progress_of_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema,'progress_of', 'project_relationship')->cvterm_id();
 359         my $project_rel_row = $schema->resultset('Project::ProjectRelationship')->find({object_project_id => $transformation_project_id, type_id => $progress_of_cvterm_id });
 360         if ($project_rel_row) {
 361             my $tracking_project_id = $project_rel_row->subject_project_id;
 362             $c->stash->{tracking_project_id} = $tracking_project_id;
 363         }
 364
 365         my $name_metadata_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'autogenerated_name_metadata', 'project_property')->cvterm_id();
 366         my $name_metadata_rs = $schema->resultset("Project::Projectprop")->find ({
 367             project_id =>  $breeding_program_data->[0]->[0],
 368             type_id => $name_metadata_cvterm_id
 369         });
 370         if($name_metadata_rs) {
 371             my $name_metadata = $name_metadata_rs->value;
 372             my $name_metadata_hash = decode_json $name_metadata;
 373             my @prefixes = keys %{$name_metadata_hash};
 374             $c->stash->{autogenerated_name_prefixes} = \@prefixes;
 375         }
 376
 377         my $transformation_project = CXGN::Transformation::Transformation->new({schema=>$schema, dbh => $c->dbc->dbh, project_id=>$transformation_project_id});
 378         my $prefix = $transformation_project->get_autogenerated_name_prefix();
 379         my $default_plant_material = $transformation_project->get_default_plant_material();
 380         my $default_plant_material_id = $default_plant_material->[0];
 381         my $default_plant_material_name = $default_plant_material->[1];
 382
 383         $c->stash->{prefix} = $prefix;
 384         $c->stash->{default_plant_material_id} = $default_plant_material_id;
 385         $c->stash->{default_plant_material_name} = $default_plant_material_name;
 386         $c->stash->{template} = '/transformation/transformation_project.mas';
 387     }
 388     else {
 389         my $field_management_factors = $c->config->{management_factor_types};
 390         my @management_factor_types = split ',',$field_management_factors;
 391         $c->stash->{management_factor_types} = \@management_factor_types;
 392         $c->stash->{trial_stock_type} = $trial->get_trial_stock_type();
 393         $c->stash->{trial_stock_count} = $trial->get_trial_stock_count();
 394         $c->stash->{template} = '/breeders_toolbox/trial.mas';
 395     }
 396
 397     print STDERR "End Load Trial Detail Page: ".localtime()."\n";
 398
 399 }
 400
 401
 402 =head2 view_by_name
 403
 404 Public Path: /breeders/trial/view_by_name/$name
 405 Path Params:
 406     name = trial unique name
 407
 408 Search for the trial that matches the provided trial name.
 409 If 1 match is found, display the trial detail page.  Display an
 410 error message if no matches are found.
 411
 412 =cut
 413
 414 sub view_trial_by_name :Path('/breeders/trial/view_by_name') CaptureArgs(1) {
 415     my ($self, $c, $trial_query) = @_;
 416     $self->search_trial($c, $trial_query);
 417 }
 418
 419
 420 sub trait_info :Path('/breeders/trial') Args(3) {
 421     my ($self, $c, $trial_id, $trait_txt, $trait_id) = @_;
 422
 423     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 424
 425     my $trial_name = $schema->resultset("Project::Project")
 426         ->search( {'me.project_id' => $trial_id})
 427         ->single
 428         ->name;
 429
 430     $c->stash->{trial_name} = $trial_name;
 431
 432     my $trait_name = $schema->resultset("Cv::Cvterm")
 433         ->search({'me.cvterm_id' => $trait_id})
 434         ->single
 435         ->name;
 436
 437     $c->stash->{trial_id}   = $trial_id;
 438     $c->stash->{trial_name} = $trial_name;
 439
 440     $c->stash->{trait_id}   = $trait_id;
 441     $c->stash->{trait_name} = $trait_name;
 442
 443     $c->stash->{template}   = '/breeders_toolbox/trial_trait.mas';
 444 }
 445
 446 ##DEPRECATED by /breeders/trials
 447 sub trial_tree : Path('/breeders/trialtree') Args(0) {
 448     my $self = shift;
 449     my $c = shift;
 450
 451
 452     $c->stash->{template} = '/breeders_toolbox/trialtree.mas';
 453
 454 }
 455
 456 #For downloading trial layout in CSV and Excel, for downloading trial phenotypes in CSV and Excel, and for downloading trial phenotyping spreadsheets in Excel.
 457 #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.
 458 sub trial_download : Chained('trial_init') PathPart('download') Args(1) {
 459     my $self = shift;
 460     my $c = shift;
 461     my $what = shift;
 462     #print STDERR "trial_download: WHAT =".Dumper($what)."\n";
 463     #print STDERR Dumper $c->req->params();
 464     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 465     my $user = $c->user();
 466     if (!$user) {
 467         $c->res->redirect( uri( path => '/user/login', query => { goto_url => $c->req->uri->path_query } ) );
 468         return;
 469     }
 470
 471     my $format = $c->req->param("format") || "xls";
 472     my $data_level = $c->req->param("dataLevel") || "plot";
 473     my $timestamp_option = $c->req->param("timestamp") || 0;
 474     my $trait_list = $c->req->param("trait_list");
 475     my $include_measured = $c->req->param('include_measured') || '';
 476     my $search_type = $c->req->param("search_type") || 'fast';
 477
 478     my $trial = $c->stash->{trial};
 479     if ($data_level eq 'plants') {
 480         if (!$trial->has_plant_entries()) {
 481             $c->stash->{template} = 'generic_message.mas';
 482             $c->stash->{message} = "The requested trial (".$trial->get_name().") does not have plant entries. Please create the plant entries first.";
 483             return;
 484         }
 485     }
 486     if ($data_level eq 'subplots' || $data_level eq 'plants_subplots') {
 487         if (!$trial->has_subplot_entries()) {
 488             $c->stash->{template} = 'generic_message.mas';
 489             $c->stash->{message} = "The requested trial (".$trial->get_name().") does not have subplot entries.";
 490             return;
 491         }
 492     }
 493
 494     my $selected_cols = $c->req->param('selected_columns') ? JSON::XS->new()->decode( $c->req->param('selected_columns') ) : {};
 495     if ($data_level eq 'plate'){
 496         $selected_cols = {'trial_name'=>1, 'acquisition_date'=>1, 'plot_name'=>1, 'plot_number'=>1, 'row_number'=>1, 'col_number'=>1, 'source_observation_unit_name'=>1, 'accession_name'=>1, 'synonyms'=>1, 'dna_person'=>1, 'notes'=>1, 'tissue_type'=>1, 'extraction'=>1, 'concentration'=>1, 'volume'=>1, 'is_blank'=>1, 'facility_identifier'=>1};
 497     }
 498     if ($data_level eq 'samplingtrial'){
 499         $selected_cols = {'trial_name'=>1, 'year'=>1, 'location'=>1, 'sampling_facility'=>1, 'sampling_trial_sample_type'=>1, 'acquisition_date'=>1, 'tissue_sample_name'=>1, 'plot_number'=>1, 'rep_number'=>1, 'source_observation_unit_name'=>1, 'accession_name'=>1, 'synonyms'=>1, 'dna_person'=>1, 'notes'=>1, 'tissue_type'=>1, 'extraction'=>1, 'concentration'=>1, 'volume'=>1 };
 500     }
 501     my $selected_trait_list_id = $c->req->param('trait_list_id');
 502     my @trait_list;
 503     if ($selected_trait_list_id){
 504         my $list = CXGN::List->new({ dbh => $c->dbc->dbh, list_id => $selected_trait_list_id });
 505         my @selected_trait_names = @{$list->elements()};
 506         my $validator = CXGN::List::Validate->new();
 507         my @absent_traits = @{$validator->validate($schema, 'traits', \@selected_trait_names)->{'missing'}};
 508         if (scalar(@absent_traits)>0){
 509             $c->stash->{template} = 'generic_message.mas';
 510             $c->stash->{message} = "Trait list is not valid because of these terms: ".join ',',@absent_traits;
 511             return;
 512         }
 513         my $lt = CXGN::List::Transform->new();
 514         @trait_list = @{$lt->transform($schema, "traits_2_trait_ids", \@selected_trait_names)->{transform}};
 515     }
 516
 517     my @treatment_project_ids;
 518     my $treatments = $trial->get_treatments();
 519     foreach (@$treatments){
 520         push @treatment_project_ids, $_->[0];
 521     }
 522
 523     if ($trait_list && $trait_list ne 'null') {
 524         @trait_list = @{_parse_list_from_json($trait_list)};
 525     }
 526
 527     my $plugin = "";
 528     if ( ($format eq "xls") && ($what eq "layout")) {
 529         $plugin = "TrialLayoutExcel";
 530     }
 531     if (($format eq "csv") && ($what eq "layout")) {
 532         $plugin = "TrialLayoutCSV";
 533     }
 534     if (($format eq "xls") && ($what =~ /phenotype/)) {
 535         $plugin = "TrialPhenotypeExcel";
 536     }
 537     if (($format eq "csv") && ($what =~ /phenotype/)) {
 538         $plugin = "TrialPhenotypeCSV";
 539     }
 540     if (($format eq "xls") && ($what eq "basic_trial_excel")) {
 541         $plugin = "BasicExcel";
 542     }
 543     if ( ($format eq "intertekxls") && ($what eq "layout")) {
 544         $plugin = "GenotypingTrialLayoutIntertekXLS";
 545     }
 546     if ( ($format eq "dartseqcsv") && ($what eq "layout")) {
 547         $plugin = "GenotypingTrialLayoutDartSeqCSV";
 548     }
 549
 550     my @field_crossing_data_order;
 551     if ($format eq "crossing_experiment_xls") {
 552         $plugin = "CrossingExperimentXLS";
 553         $what = "crosses";
 554         $format = "xlsx";
 555         my $cross_properties = $c->config->{cross_properties};
 556         @field_crossing_data_order = split ',',$cross_properties;
 557     }
 558
 559     my $prop_id;
 560     if ($format eq "soil_data_xls") {
 561         $plugin = "SoilDataXLS";
 562         $what = "soil_data";
 563         $format = "xlsx";
 564         $prop_id = $c->req->param("prop_id");
 565     }
 566
 567     my $trial_name = $trial->get_name();
 568     $trial_name =~ s/ /\_/g;
 569     my $trial_id = $trial->get_trial_id();
 570     my $dir = $c->tempfiles_subdir('download');
 571     my $temp_file_name = $trial_name . "_" . "$what" . "XXXX";
 572     my $rel_file = $c->tempfile( TEMPLATE => "download/$temp_file_name");
 573     $rel_file = $rel_file . ".$format";
 574     my $tempfile = $c->config->{basepath}."/".$rel_file;
 575
 576
 577     my $download = CXGN::Trial::Download->new({
 578         bcs_schema => $schema,
 579         trial_id => $c->stash->{trial_id},
 580         trait_list => \@trait_list,
 581         filename => $tempfile,
 582         format => $plugin,
 583         data_level => $data_level,
 584         search_type => $search_type,
 585         include_timestamp => $timestamp_option,
 586         treatment_project_ids => \@treatment_project_ids,
 587         selected_columns => $selected_cols,
 588         include_measured => $include_measured,
 589         field_crossing_data_order => \@field_crossing_data_order,
 590         prop_id => $prop_id
 591     });
 592
 593     my $error = $download->download();
 594
 595     if ($format eq 'intertekxls'){
 596         $format = 'xls';
 597     }
 598     if ($format eq 'dartseqcsv'){
 599         $format = 'csv';
 600     }
 601
 602     #my $file_name = $trial_id . "_" . "$what" . ".$format";
 603     my $file_name = $trial_name . "_" . "layout" . ".$format";
 604     $c->res->content_type('Application/'.$format);
 605     $c->res->header('Content-Disposition', qq[attachment; filename="$file_name"]);
 606
 607     my $output = read_file($tempfile);
 608
 609     $c->res->body($output);
 610 }
 611
 612 sub trials_download_layouts : Path('/breeders/trials/download/layout') Args(0) {
 613     my $self = shift;
 614     my $c = shift;
 615     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 616     my $user = $c->user();
 617     if (!$user) {
 618         $c->res->redirect( uri( path => '/user/login', query => { goto_url => $c->req->uri->path_query } ) );
 619         return;
 620     }
 621
 622     my $format = $c->req->param("format") || "xls";
 623     my $data_level = $c->req->param("dataLevel") || "plot";
 624     my $genotyping_trial_id = $c->req->param("genotyping_trial_id");
 625     my @genotyping_trial_id_list = $c->req->param("genotyping_trial_id_list") ? split ',', $c->req->param("genotyping_trial_id_list") : ();
 626
 627     my $selected_cols = $c->req->param('selected_columns') ? JSON::XS->new()->decode( $c->req->param('selected_columns') ) : {};
 628     if ($data_level eq 'plate'){
 629         $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,
 630         'accession_name'=>1, 'synonyms'=>1, 'dna_person'=>1, 'notes'=>1, 'tissue_type'=>1, 'extraction'=>1, 'concentration'=>1, 'volume'=>1, 'is_blank'=>1, 'facility_identifier' =>1};
 631     }
 632
 633     my $plugin = "";
 634     if ($format eq "intertekxls") {
 635         $plugin = "GenotypingTrialLayoutIntertekXLS";
 636     }
 637     if ($format eq "dartseqcsv") {
 638         $plugin = "GenotypingTrialLayoutDartSeqCSV";
 639     }
 640     if ($format eq "csv") {
 641         $plugin = "TrialLayoutCSV";
 642     }
 643
 644     my $dir = $c->tempfiles_subdir('download');
 645     my $temp_file_name = "genotyping_plate_layouts"."XXXX";
 646     my $rel_file = $c->tempfile( TEMPLATE => "download/$temp_file_name");
 647     $rel_file = $rel_file . ".$format";
 648     my $tempfile = $c->config->{basepath}."/".$rel_file;
 649
 650     #print STDERR "TEMPFILE : $tempfile\n";
 651
 652     my $trial_download_args = {
 653         bcs_schema => $schema,
 654         trial_list => \@genotyping_trial_id_list,
 655         filename => $tempfile,
 656         format => $plugin,
 657         data_level => $data_level,
 658         selected_columns => $selected_cols
 659     };
 660     if ($genotyping_trial_id) {
 661         $trial_download_args->{trial_id} = $genotyping_trial_id;
 662     }
 663     my $download = CXGN::Trial::Download->new($trial_download_args);
 664     my $error = $download->download();
 665
 666     if ($format eq 'intertekxls'){
 667         $format = 'xls';
 668     }
 669     if ($format eq 'dartseqcsv'){
 670         $format = 'csv';
 671     }
 672
 673     my $file_name = "genotyping_plate_layouts.$format";
 674     $c->res->content_type('Application/'.$format);
 675     $c->res->header('Content-Disposition', qq[attachment; filename="$file_name"]);
 676     my $output = read_file($tempfile);
 677     $c->res->body($output);
 678 }
 679
 680 sub _parse_list_from_json {
 681     my $list_json = shift;
 682
 683     if ($list_json) {
 684         #my $decoded_list = $json->allow_nonref->relaxed->escape_slash->loose->allow_singlequote->allow_barekey->decode($list_json);
 685         my $decoded_list = JSON::XS->new()->decode($list_json);
 686         my @array_of_list_items = @{$decoded_list};
 687         return \@array_of_list_items;
 688     }
 689     else {
 690         return;
 691     }
 692 }
 693
 694
 695 # Search for trial by trial name
 696 # Display trial detail page for 1 match, error messages for no matches
 697 sub search_trial : Private {
 698     my ( $self, $c, $trial_query ) = @_;
 699     my $schema = $c->dbic_schema("Bio::Chado::Schema");
 700     my $rs = $schema->resultset('Project::Project');
 701
 702     my $matches;
 703     my $count = 0;
 704
 705     # Search by name
 706     if ( defined($trial_query) ) {
 707         $matches = $rs->search({
 708                 'UPPER(name)' => uc($trial_query)
 709             }
 710         );
 711         $count = $matches->count;
 712     }
 713
 714     # NO MATCH FOUND
 715     if ( $count != 1 ) {
 716         $c->stash->{template} = "generic_message.mas";
 717         $c->stash->{message} = "<strong>No Matching Trial Found</strong> ($trial_query)<br />You can view and search for trials from the <a href='/search/trials'>Trial Search Page</a>";
 718     }
 719
 720     # 1 MATCH FOUND - FORWARD TO VIEW TRIAL
 721     else {
 722         my $trial_id = $matches->first->project_id;
 723         $c->stash->{trial_id} = $trial_id;
 724
 725         my $schema = $c->dbic_schema("Bio::Chado::Schema");
 726         $c->stash->{schema} = $schema;
 727
 728         my $trial = CXGN::Trial->new( { bcs_schema => $schema, trial_id => $trial_id });
 729         $c->stash->{trial} = $trial;
 730
 731         $c->forward('trial_info');
 732     }
 733 }
 734
 735
 736 1;