lib/SGN/Controller/BreedersToolbox.pm

   1
   2 package SGN::Controller::BreedersToolbox;
   3
   4 use Moose;
   5
   6 use Data::Dumper;
   7 use SGN::Controller::AJAX::List;
   8 use CXGN::List::Transform;
   9 use CXGN::BreedersToolbox::Projects;
  10 use CXGN::BreedersToolbox::Accessions;
  11 use SGN::Model::Cvterm;
  12 use URI::FromHash 'uri';
  13 use Spreadsheet::WriteExcel;
  14 use Spreadsheet::Read;
  15 use File::Slurp qw | read_file |;
  16 use File::Temp;
  17 use CXGN::Trial::TrialLayout;
  18 use Try::Tiny;
  19 use File::Basename qw | basename dirname|;
  20 use File::Spec::Functions;
  21 use CXGN::People::Roles;
  22 use CXGN::Trial::TrialLayout;
  23 use CXGN::Genotype::Search;
  24 use CXGN::Trial;
  25
  26
  27 BEGIN { extends 'Catalyst::Controller'; }
  28
  29 sub manage_breeding_programs : Path("/breeders/manage_programs") :Args(0) {
  30     my $self = shift;
  31     my $c = shift;
  32
  33     if (!$c->user()) {
  34
  35         # redirect to login page
  36         $c->res->redirect( uri( path => '/user/login', query => { goto_url => $c->req->uri->path_query } ) );
  37         return;
  38     }
  39
  40     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
  41
  42     my $projects = CXGN::BreedersToolbox::Projects->new( { schema=> $schema } );
  43
  44     my $breeding_programs = $projects->get_breeding_programs();
  45
  46     $c->stash->{breeding_programs} = $breeding_programs;
  47     $c->stash->{user} = $c->user();
  48
  49     $c->stash->{template} = '/breeders_toolbox/breeding_programs.mas';
  50
  51
  52 }
  53
  54 sub manage_trials : Path("/breeders/trials") Args(0) {
  55     my $self = shift;
  56     my $c = shift;
  57
  58     if (!$c->user()) {
  59
  60         # redirect to login page
  61         $c->res->redirect( uri( path => '/user/login', query => { goto_url => $c->req->uri->path_query } ) );
  62         return;
  63     }
  64
  65     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
  66
  67     my $projects = CXGN::BreedersToolbox::Projects->new( { schema=> $schema } );
  68
  69     my @editable_stock_props = split ',', $c->config->{editable_stock_props};
  70     my %editable_stock_props = map { $_=>1 } @editable_stock_props;
  71
  72     my @editable_stock_props_definitions = split ',', $c->config->{editable_stock_props_definitions};
  73     my %def_hash;
  74     foreach (@editable_stock_props_definitions) {
  75         my @term_def = split ':', $_;
  76         $def_hash{$term_def[0]} = $term_def[1];
  77     }
  78
  79     my $breeding_programs = $projects->get_breeding_programs();
  80     my @breeding_programs = @$breeding_programs;
  81     my @roles = $c->user->roles();
  82
  83     #Add true false field to breeding program array indicating whether program is linked to current user
  84     foreach my $role (@roles) {
  85         for (my $i=0; $i < scalar @breeding_programs; $i++) {
  86             if ($role eq $breeding_programs[$i][1]){
  87                 $breeding_programs[$i][3] = 1;
  88             } else {
  89                 $breeding_programs[$i][3] = 0;
  90             }
  91         }
  92     }
  93
  94     #print STDERR "Breeding programs are ".Dumper(@breeding_programs);
  95     my $field_management_factors = $c->config->{management_factor_types};
  96     my @management_factor_types = split ',',$field_management_factors;
  97
  98     my $design_type_string = $c->config->{design_types};
  99     my @design_types = split ',',$design_type_string;
 100
 101     $c->stash->{design_types} = \@design_types;
 102     $c->stash->{management_factor_types} = \@management_factor_types;
 103     $c->stash->{editable_stock_props} = \%editable_stock_props;
 104     $c->stash->{editable_stock_props_definitions} = \%def_hash;
 105     $c->stash->{preferred_species} = $c->config->{preferred_species};
 106     $c->stash->{timestamp} = localtime;
 107
 108     my $locations = $projects->get_all_locations_by_breeding_program();
 109
 110     #print STDERR "Locations are ".Dumper($locations)."\n";
 111
 112     $c->stash->{locations} = $locations;
 113
 114     $c->stash->{breeding_programs} = \@breeding_programs;
 115
 116     $c->stash->{template} = '/breeders_toolbox/manage_projects.mas';
 117 }
 118
 119 sub manage_accessions : Path("/breeders/accessions") Args(0) {
 120     my $self = shift;
 121     my $c = shift;
 122     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 123     my $list_id = $c->req->param('list_id') || ''; #If a list_id is given in the URL, then the add accessions process will automatically begin with that list.
 124
 125     if (!$c->user()) {
 126         # redirect to login page
 127         #
 128         $c->res->redirect( uri( path => '/user/login', query => { goto_url => $c->req->uri->path_query } ) );
 129         return;
 130     }
 131
 132     my $ac = CXGN::BreedersToolbox::Accessions->new( { schema=>$schema });
 133
 134     my $accessions = $ac->get_all_accessions($c);
 135     # my $populations = $ac->get_all_populations($c);
 136
 137     my @editable_stock_props = split ',', $c->config->{editable_stock_props};
 138     my %editable_stock_props = map { $_=>1 } @editable_stock_props;
 139
 140     my @editable_stock_props_definitions = split ',', $c->config->{editable_stock_props_definitions};
 141     my %def_hash;
 142     foreach (@editable_stock_props_definitions) {
 143         my @term_def = split ':', $_;
 144         $def_hash{$term_def[0]} = $term_def[1];
 145     }
 146
 147     $c->stash->{accessions} = $accessions;
 148     $c->stash->{list_id} = $list_id;
 149     #$c->stash->{population_groups} = $populations;
 150     $c->stash->{preferred_species} = $c->config->{preferred_species};
 151     $c->stash->{editable_stock_props} = \%editable_stock_props;
 152     $c->stash->{editable_stock_props_definitions} = \%def_hash;
 153     $c->stash->{template} = '/breeders_toolbox/manage_accessions.mas';
 154 }
 155
 156 sub manage_roles : Path("/breeders/manage_roles") Args(0) {
 157     my $self = shift;
 158     my $c = shift;
 159
 160     if (!$c->user()) {
 161         $c->res->redirect( uri( path => '/user/login', query => { goto_url => $c->req->uri->path_query } ) );
 162         return;
 163     }
 164
 165     $c->stash->{is_curator} = $c->user->check_roles("curator");
 166
 167     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 168     my $person_roles = CXGN::People::Roles->new({ bcs_schema=>$schema });
 169     my $ascii_chars = 1;
 170     my $breeding_programs = $person_roles->get_breeding_program_roles($ascii_chars);
 171
 172     $c->stash->{roles} = $breeding_programs;
 173     $c->stash->{template} = '/breeders_toolbox/manage_roles.mas';
 174 }
 175
 176 sub manage_tissue_samples : Path("/breeders/samples") Args(0) {
 177     my $self = shift;
 178     my $c = shift;
 179
 180     if (!$c->user()) {
 181         $c->res->redirect( uri( path => '/user/login', query => { goto_url => $c->req->uri->path_query } ) );
 182         return;
 183     }
 184     my $genotyping_facilities = $c->config->{genotyping_facilities};
 185     my @facilities = split ',',$genotyping_facilities;
 186
 187     my $sampling_facilities = $c->config->{sampling_facilities};
 188     my @sampling_facilities = split ',',$sampling_facilities;
 189
 190     $c->stash->{facilities} = \@facilities;
 191     $c->stash->{sampling_facilities} = \@sampling_facilities;
 192     $c->stash->{user_id} = $c->user()->get_object()->get_sp_person_id();
 193     $c->stash->{template} = '/breeders_toolbox/manage_samples.mas';
 194 }
 195
 196
 197 sub manage_locations : Path("/breeders/locations") Args(0) {
 198     my $self = shift;
 199     my $c = shift;
 200
 201     if (!$c->user()) {
 202
 203         # redirect to login page
 204         #
 205         $c->res->redirect( uri( path => '/user/login', query => { goto_url => $c->req->uri->path_query } ) );
 206         return;
 207     }
 208
 209     $c->stash->{user_id} = $c->user()->get_object()->get_sp_person_id();
 210
 211     $c->stash->{template} = '/breeders_toolbox/manage_locations.mas';
 212 }
 213
 214 sub manage_nurseries : Path("/breeders/nurseries") Args(0) {
 215     my $self = shift;
 216     my $c = shift;
 217
 218     if (!$c->user()) {
 219
 220         # redirect to login page
 221         #
 222         $c->res->redirect( uri( path => '/user/login', query => { goto_url => $c->req->uri->path_query } ) );
 223         return;
 224     }
 225     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 226     my $bp = CXGN::BreedersToolbox::Projects->new( { schema=>$schema });
 227     my $breeding_programs = $bp->get_breeding_programs();
 228
 229     $c->stash->{user_id} = $c->user()->get_object()->get_sp_person_id();
 230
 231     $c->stash->{locations} = $bp->get_all_locations($c);
 232
 233     #$c->stash->{projects} = $self->get_projects($c);
 234
 235     $c->stash->{programs} = $breeding_programs;
 236
 237     $c->stash->{roles} = $c->user()->roles();
 238
 239     $c->stash->{nurseries} = $self->get_nurseries($c);
 240
 241     $c->stash->{template} = '/breeders_toolbox/manage_nurseries.mas';
 242
 243 }
 244
 245 sub manage_crosses : Path("/breeders/crosses") Args(0) {
 246     my $self = shift;
 247     my $c = shift;
 248
 249     if (!$c->user()) {
 250
 251         # redirect to login page
 252         #
 253         $c->res->redirect( uri( path => '/user/login', query => { goto_url => $c->req->uri->path_query } ) );
 254         return;
 255     }
 256     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 257     my $bp = CXGN::BreedersToolbox::Projects->new( { schema=>$schema });
 258     my $breeding_programs = $bp->get_breeding_programs();
 259
 260     my $crossingtrial = CXGN::BreedersToolbox::Projects->new( { schema=>$schema });
 261     my $crossing_trials = $crossingtrial->get_crossing_trials();
 262
 263     $c->stash->{user_id} = $c->user()->get_object()->get_sp_person_id();
 264
 265
 266     my @breeding_programs = @$breeding_programs;
 267     my @roles = $c->user->roles();
 268
 269     foreach my $role (@roles) {
 270         for (my $i=0; $i < scalar @breeding_programs; $i++) {
 271             if ($role eq $breeding_programs[$i][1]){
 272                 $breeding_programs[$i][3] = 1;
 273             } else {
 274                 $breeding_programs[$i][3] = 0;
 275             }
 276         }
 277     }
 278
 279     my $locations = $crossingtrial->get_all_locations_by_breeding_program();
 280
 281     $c->stash->{locations} = $locations;
 282
 283     $c->stash->{programs} = \@breeding_programs;
 284
 285     #$c->stash->{locations} = $bp->get_all_locations($c);
 286
 287     #$c->stash->{programs} = $breeding_programs;
 288
 289     $c->stash->{crossing_trials} = $crossing_trials;
 290
 291     $c->stash->{roles} = $c->user()->roles();
 292
 293     $c->stash->{template} = '/breeders_toolbox/manage_crosses.mas';
 294
 295 }
 296
 297 sub manage_phenotyping :Path("/breeders/phenotyping") Args(0) {
 298     my $self =shift;
 299     my $c = shift;
 300
 301     if (!$c->user()) {
 302         $c->res->redirect( uri( path => '/user/login', query => { goto_url => $c->req->uri->path_query } ) );
 303         return;
 304     }
 305
 306     my @file_types = ( 'spreadsheet phenotype file', 'direct phenotyping', 'trial_additional_file_upload', 'brapi observations', 'tablet phenotype file' );
 307     my $data = $self->get_file_data($c, \@file_types);
 308
 309     $c->stash->{phenotype_files} = $data->{files};
 310     $c->stash->{deleted_phenotype_files} = $data->{deleted_files};
 311
 312     $c->stash->{template} = '/breeders_toolbox/manage_phenotyping.mas';
 313
 314 }
 315
 316 sub manage_nirs :Path("/breeders/nirs") Args(0) {
 317     my $self =shift;
 318     my $c = shift;
 319
 320     if (!$c->user()) {
 321         $c->res->redirect( uri( path => '/user/login', query => { goto_url => $c->req->uri->path_query } ) );
 322         return;
 323     }
 324
 325     my @file_types = ( 'nirs spreadsheet' );
 326     my $all_data = $self->get_file_data($c, \@file_types, 1);
 327     my $data = $self->get_file_data($c, \@file_types, 0);
 328
 329     my $sampling_facilities = $c->config->{sampling_facilities};
 330     my @sampling_facilities = split ',',$sampling_facilities;
 331
 332     $c->stash->{sampling_facilities} = \@sampling_facilities;
 333     $c->stash->{nirs_files} = $data->{files};
 334     $c->stash->{deleted_nirs_files} = $data->{deleted_files};
 335     $c->stash->{all_nirs_files} = $all_data->{files};
 336     $c->stash->{all_deleted_nirs_files} = $all_data->{deleted_files};
 337
 338     $c->stash->{template} = '/breeders_toolbox/manage_nirs.mas';
 339
 340 }
 341
 342 sub manage_upload :Path("/breeders/upload") Args(0) {
 343     my $self =shift;
 344     my $c = shift;
 345     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 346
 347     if (!$c->user()) {
 348         $c->res->redirect( uri( path => '/user/login', query => { goto_url => $c->req->uri->path_query } ) );
 349         return;
 350     }
 351
 352     my @editable_stock_props = split ',', $c->config->{editable_stock_props};
 353     my %editable_stock_props = map { $_=>1 } @editable_stock_props;
 354
 355     my @editable_stock_props_definitions = split ',', $c->config->{editable_stock_props_definitions};
 356     my %def_hash;
 357     foreach (@editable_stock_props_definitions) {
 358         my @term_def = split ':', $_;
 359         $def_hash{$term_def[0]} = $term_def[1];
 360     }
 361
 362     my $projects = CXGN::BreedersToolbox::Projects->new( { schema=> $schema } );
 363     my $breeding_programs = $projects->get_breeding_programs();
 364
 365     my $genotyping_facilities = $c->config->{genotyping_facilities};
 366     my @facilities = split ',',$genotyping_facilities;
 367
 368     my $field_management_factors = $c->config->{management_factor_types};
 369     my @management_factor_types = split ',',$field_management_factors;
 370
 371     my $design_type_string = $c->config->{design_types};
 372     my @design_types = split ',',$design_type_string;
 373
 374     $c->stash->{editable_stock_props} = \%editable_stock_props;
 375     $c->stash->{editable_stock_props_definitions} = \%def_hash;
 376     $c->stash->{design_types} = \@design_types;
 377     $c->stash->{management_factor_types} = \@management_factor_types;
 378     $c->stash->{facilities} = \@facilities;
 379     $c->stash->{geojson_locations} = $projects->get_all_locations_by_breeding_program();
 380     $c->stash->{locations} = $projects->get_all_locations();
 381     $c->stash->{breeding_programs} = $breeding_programs;
 382     $c->stash->{timestamp} = localtime;
 383     $c->stash->{preferred_species} = $c->config->{preferred_species};
 384     $c->stash->{template} = '/breeders_toolbox/manage_upload.mas';
 385 }
 386
 387 sub manage_file_share_dump :Path("/breeders/file_share_dump") Args(0) {
 388     my $self =shift;
 389     my $c = shift;
 390     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 391
 392     if (!$c->user()) {
 393         $c->res->redirect( uri( path => '/user/login', query => { goto_url => $c->req->uri->path_query } ) );
 394         return;
 395     }
 396
 397     $c->stash->{template} = '/breeders_toolbox/file_share/manage_file_share_dump.mas';
 398 }
 399
 400 sub manage_plot_phenotyping :Path("/breeders/plot_phenotyping") Args(0) {
 401     my $self =shift;
 402     my $c = shift;
 403     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 404     my $stock_id = $c->req->param('stock_id');
 405
 406     if (!$c->user()) {
 407              $c->res->redirect( uri( path => '/user/login', query => { goto_url => $c->req->uri->path_query } ) );
 408               return;
 409     }
 410     my $stock = $schema->resultset("Stock::Stock")->find( { stock_id=>$stock_id })->uniquename();
 411
 412     $c->stash->{plot_name} = $stock;
 413     $c->stash->{stock_id} = $stock_id;
 414     $c->stash->{template} = '/breeders_toolbox/manage_plot_phenotyping.mas';
 415
 416 }
 417
 418 sub manage_trial_phenotyping :Path("/breeders/trial_phenotyping") Args(0) {
 419     my $self =shift;
 420     my $c = shift;
 421     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 422     my $trial_id = $c->req->param('trial_id');
 423
 424     if (!$c->user()) {
 425              $c->res->redirect( uri( path => '/user/login', query => { goto_url => $c->req->uri->path_query } ) );
 426               return;
 427     }
 428     my $project_name = $schema->resultset("Project::Project")->find( { project_id=>$trial_id })->name();
 429
 430     my $trial = CXGN::Trial->new({ bcs_schema => $schema, trial_id => $trial_id });
 431
 432     $c->stash->{trial_stock_type} = $trial->get_trial_stock_type();
 433     $c->stash->{trial_name} = $project_name;
 434     $c->stash->{trial_id} = $trial_id;
 435     $c->stash->{template} = '/breeders_toolbox/manage_trial_phenotyping.mas';
 436 }
 437
 438 sub manage_odk_data_collection :Path("/breeders/odk") Args(0) {
 439     my $self =shift;
 440     my $c = shift;
 441     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 442
 443     if (!$c->user()) {
 444         $c->res->redirect( uri( path => '/user/login', query => { goto_url => $c->req->uri->path_query } ) );
 445         return;
 446     }
 447     $c->stash->{odk_crossing_data_service_name} = $c->config->{odk_crossing_data_service_name};
 448     $c->stash->{odk_crossing_data_service_url} = $c->config->{odk_crossing_data_service_url};
 449     $c->stash->{odk_crossing_data_test_form_name} = $c->config->{odk_crossing_data_test_form_name};
 450     $c->stash->{odk_phenotyping_data_service_name} = $c->config->{odk_phenotyping_data_service_name};
 451     $c->stash->{odk_phenotyping_data_service_url} = $c->config->{odk_phenotyping_data_service_url};
 452     $c->stash->{template} = '/breeders_toolbox/manage_odk_data_collection.mas';
 453 }
 454
 455
 456 sub manage_identifier_generation :Path("/breeders/identifier_generation") Args(0) {
 457     my $self =shift;
 458     my $c = shift;
 459     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 460
 461     if (!$c->user()) {
 462         $c->res->redirect( uri( path => '/user/login', query => { goto_url => $c->req->uri->path_query } ) );
 463         return;
 464     }
 465     $c->stash->{template} = '/breeders_toolbox/identifier_generation/manage_identifier_generation.mas';
 466 }
 467
 468
 469 sub manage_phenotyping_download : Path("/breeders/phenotyping/download") Args(1) {
 470     my $self =shift;
 471     my $c = shift;
 472     my $file_id = shift;
 473
 474     my $metadata_schema = $c->dbic_schema('CXGN::Metadata::Schema');
 475     my $file_row = $metadata_schema->resultset("MdFiles")->find({file_id => $file_id});
 476     my $file_destination =  catfile($file_row->dirname, $file_row->basename);
 477     #print STDERR "\n\n\nfile name:".$file_row->basename."\n";
 478     my $contents = read_file($file_destination);
 479     my $file_name = $file_row->basename;
 480     $c->res->content_type('Application/trt');
 481     $c->res->header('Content-Disposition', qq[attachment; filename="$file_name"]);
 482     $c->res->body($contents);
 483 }
 484
 485 sub manage_phenotyping_view : Path("/breeders/phenotyping/view") Args(1) {
 486     my $self =shift;
 487     my $c = shift;
 488     my $file_id = shift;
 489
 490     my $metadata_schema = $c->dbic_schema('CXGN::Metadata::Schema');
 491     my $file_row = $metadata_schema->resultset("MdFiles")->find({file_id => $file_id});
 492     my $file_destination =  catfile($file_row->dirname, $file_row->basename);
 493     #print STDERR "\n\n\nfile name:".$file_row->basename."\n";
 494     my @contents = ReadData ($file_destination);
 495     #print STDERR Dumper \@contents;
 496     my $file_name = $file_row->basename;
 497     $c->stash->{file_content} = \@contents;
 498     $c->stash->{filename} = $file_name;
 499     $c->stash->{template} = '/breeders_toolbox/view_file.mas';
 500 }
 501
 502 sub make_cross_form :Path("/stock/cross/new") :Args(0) {
 503     my ($self, $c) = @_;
 504     $c->stash->{template} = '/breeders_toolbox/new_cross.mas';
 505     if ($c->user()) {
 506       my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 507       # get projects
 508       my @rows = $schema->resultset('Project::Project')->all();
 509       my @projects = ();
 510       foreach my $row (@rows) {
 511         push @projects, [ $row->project_id, $row->name, $row->description ];
 512       }
 513       $c->stash->{project_list} = \@projects;
 514       @rows = $schema->resultset('NaturalDiversity::NdGeolocation')->all();
 515       my @locations = ();
 516       foreach my $row (@rows) {
 517         push @locations,  [ $row->nd_geolocation_id,$row->description ];
 518       }
 519       $c->stash->{locations} = \@locations;
 520
 521     }
 522     else {
 523       $c->res->redirect( uri( path => '/user/login', query => { goto_url => $c->req->uri->path_query } ) );
 524       return;
 525     }
 526 }
 527
 528
 529 sub make_cross :Path("/stock/cross/generate") :Args(0) {
 530     my ($self, $c) = @_;
 531     $c->stash->{template} = '/breeders_toolbox/progeny_from_crosses.mas';
 532     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 533     my $cross_name = $c->req->param('cross_name');
 534     $c->stash->{cross_name} = $cross_name;
 535     my $trial_id = $c->req->param('trial_id');
 536     $c->stash->{trial_id} = $trial_id;
 537     #my $location = $c->req->param('location_id');
 538     my $maternal = $c->req->param('maternal');
 539     my $paternal = $c->req->param('paternal');
 540     my $prefix = $c->req->param('prefix');
 541     my $suffix = $c->req->param('suffix');
 542     my $progeny_number = $c->req->param('progeny_number');
 543     my $visible_to_role = $c->req->param('visible_to_role');
 544
 545     if (! $c->user()) { # redirect
 546         $c->res->redirect( uri( path => '/user/login', query => { goto_url => $c->req->uri->path_query } ) );
 547         return;
 548     }
 549
 550
 551     #check that progeny number is an integer less than maximum allowed
 552     my $maximum_progeny_number = 1000;
 553     if ((! $progeny_number =~ m/^\d+$/) or ($progeny_number > $maximum_progeny_number)){
 554       #redirect to error page?
 555       return;
 556     }
 557
 558     #check that parent names are not blank
 559     if ($maternal eq "" or $paternal eq "") {
 560       return;
 561     }
 562
 563     #check that parents exist in the database
 564     if (! $schema->resultset("Stock::Stock")->find({name=>$maternal,})){
 565       return;
 566     }
 567     if (! $schema->resultset("Stock::Stock")->find({name=>$paternal,})){
 568       return;
 569     }
 570
 571     #check that cross name does not already exist
 572     if ($schema->resultset("Stock::Stock")->find({name=>$cross_name})){
 573       return;
 574     }
 575
 576     #check that progeny do not already exist
 577     if ($schema->resultset("Stock::Stock")->find({name=>$prefix.$cross_name.$suffix."-1",})){
 578       return;
 579     }
 580
 581     my $organism = $schema->resultset("Organism::Organism")->find_or_create(
 582     {
 583         genus   => 'Manihot',
 584         species => 'Manihot esculenta',
 585     } );
 586     my $organism_id = $organism->organism_id();
 587
 588     my $accession_cvterm = SGN::Model::Cvterm->get_cvterm_row($schema, 'accession', 'stock_type');
 589
 590     my $population_cvterm = $schema->resultset("Cv::Cvterm")->find(
 591       { name   => 'population',
 592     });
 593
 594
 595     my $female_parent_stock = $schema->resultset("Stock::Stock")->find(
 596         { name       => $maternal,
 597         } );
 598
 599     my $male_parent_stock = $schema->resultset("Stock::Stock")->find(
 600             { name       => $paternal,
 601             } );
 602
 603     my $population_stock = $schema->resultset("Stock::Stock")->find_or_create(
 604             { organism_id => $organism_id,
 605               name       => $cross_name,
 606               uniquename => $cross_name,
 607               type_id => $population_cvterm->cvterm_id,
 608             } );
 609       my $female_parent =  SGN::Model::Cvterm->get_cvterm_row($schema, 'female_parent',  'stock_relationship');
 610
 611       my $male_parent =  SGN::Model::Cvterm->get_cvterm_row($schema, 'male_parent', 'stock_relationship');
 612
 613
 614       my $population_members =  SGN::Model::Cvterm->get_cvterm_row($schema,  'cross_relationship','stock_relationship');
 615
 616
 617     my $visible_to_role_cvterm =  SGN::Model::Cvterm->get_cvterm_row($schema,  'visible_to_role', 'local');
 618
 619     my $increment = 1;
 620     while ($increment < $progeny_number + 1) {
 621         $increment = sprintf "%03d", $increment;
 622         my $stock_name = $prefix.$cross_name."_".$increment.$suffix;
 623       my $accession_stock = $schema->resultset("Stock::Stock")->create(
 624             { organism_id => $organism_id,
 625               name       => $stock_name,
 626               uniquename => $stock_name,
 627               type_id     => $accession_cvterm->cvterm_id,
 628             } );
 629       $accession_stock->find_or_create_related('stock_relationship_objects', {
 630                 type_id => $female_parent->cvterm_id(),
 631                 object_id => $accession_stock->stock_id(),
 632                 subject_id => $female_parent_stock->stock_id(),
 633                                                   } );
 634       $accession_stock->find_or_create_related('stock_relationship_objects', {
 635                 type_id => $male_parent->cvterm_id(),
 636                 object_id => $accession_stock->stock_id(),
 637                 subject_id => $male_parent_stock->stock_id(),
 638                                                   } );
 639       $accession_stock->find_or_create_related('stock_relationship_objects', {
 640                 type_id => $population_members->cvterm_id(),
 641                 object_id => $accession_stock->stock_id(),
 642                 subject_id => $population_stock->stock_id(),
 643                                                   } );
 644       if ($visible_to_role ne "") {
 645         my $accession_stock_prop = $schema->resultset("Stock::Stockprop")->find_or_create(
 646                { type_id =>$visible_to_role_cvterm->cvterm_id(),
 647                  value => $visible_to_role,
 648                  stock_id => $accession_stock->stock_id()
 649                  });
 650       }
 651       $increment++;
 652
 653     }
 654     if ($@) {
 655     }
 656 }
 657
 658 sub selection_index : Path("/selection/index") :Args(0) {
 659     my $self = shift;
 660     my $c = shift;
 661
 662     if (!$c->user()) {
 663
 664         # redirect to login page
 665         $c->res->redirect( uri( path => '/user/login', query => { goto_url => $c->req->uri->path_query } ) );
 666         return;
 667     }
 668
 669 #    my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 670
 671   #  my $projects = CXGN::BreedersToolbox::Projects->new( { schema=> $schema } );
 672
 673 #    my $breeding_programs = $projects->get_breeding_programs();
 674
 675   #  $c->stash->{breeding_programs} = $breeding_programs;
 676     $c->stash->{user} = $c->user();
 677
 678     $c->stash->{template} = '/breeders_toolbox/selection_index.mas';
 679
 680
 681 }
 682
 683
 684 sub breeder_home :Path("/breeders/home") Args(0) {
 685     my ($self , $c) = @_;
 686
 687
 688     if (!$c->user()) {
 689
 690         # redirect to login page
 691         $c->res->redirect( uri( path => '/user/login', query => { goto_url => $c->req->uri->path_query } ) );
 692         return;
 693     }
 694
 695     # my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 696     # my $bp = CXGN::BreedersToolbox::Projects->new( { schema=>$schema });
 697     # my $breeding_programs = $bp->get_breeding_programs();
 698
 699     # $c->stash->{programs} = $breeding_programs;
 700     # $c->stash->{breeding_programs} = $breeding_programs;
 701
 702     # # my $locations_by_breeding_program;
 703     # # foreach my $b (@$breeding_programs) {
 704     # #     $locations_by_breeding_program->{$b->[1]} = $bp->get_locations_by_breeding_program($b->[0]);
 705     # # }
 706     # # $locations_by_breeding_program->{'Other'} = $bp->get_locations_by_breeding_program();
 707
 708     # $c->stash->{locations_by_breeding_program} = ""; #$locations_by_breeding_program;
 709
 710     # # get roles
 711     # #
 712     # my @roles = $c->user->roles();
 713     # $c->stash->{roles}=\@roles;
 714
 715     # $c->stash->{stockrelationships} = $self->get_stock_relationships($c);
 716
 717     # my $locations = $bp->get_locations($c);
 718
 719     # $c->stash->{locations} = $locations;
 720     # # get uploaded phenotype files
 721     # #
 722
 723     # my $data = $self->get_file_data($c, \@file_types);
 724
 725     # $c->stash->{phenotype_files} = $data->{file_info};
 726     # $c->stash->{deleted_phenotype_files} = $data->{deleted_file_info};
 727
 728
 729     $c->stash->{template} = '/breeders_toolbox/home.mas';
 730 }
 731
 732 sub breeder_search : Path('/breeders/search/') :Args(0) {
 733     my ($self, $c) = @_;
 734
 735     if (!$c->user()) {
 736         $c->res->redirect( uri( path => '/user/login', query => { goto_url => $c->req->uri->path_query } ) );
 737         return;
 738     }
 739
 740     $c->stash->{dataset_id} = $c->req->param('dataset_id');
 741     $c->stash->{template} = '/breeders_toolbox/breeder_search_page.mas';
 742
 743 }
 744 sub get_file_data : Private {
 745     my $self = shift;
 746     my $c = shift;
 747     my $file_types = shift;
 748     my $get_files_for_all_users = shift;
 749     my $file_type_string = "'".join("','", @$file_types)."'";
 750
 751     my $metadata_schema = $c->dbic_schema("CXGN::Metadata::Schema");
 752
 753     my $file_info = [];
 754     my $deleted_file_info = [];
 755
 756     my $where_string = '';
 757     if (!$get_files_for_all_users) {
 758         $where_string = ' AND md.create_person_id = '.$c->user()->get_object->get_sp_person_id();
 759     }
 760
 761     my $q = "SELECT mdf.file_id, mdf.basename, mdf.dirname, mdf.filetype, mdf.md5checksum, md.create_date, md.obsolete
 762         FROM metadata.md_files AS mdf
 763         JOIN metadata.md_metadata AS md ON (mdf.metadata_id = md.metadata_id)
 764         WHERE mdf.filetype IN ($file_type_string) $where_string;";
 765     print STDERR $q."\n";
 766     my $h = $c->dbc->dbh->prepare($q);
 767     $h->execute();
 768     while (my ($file_id, $basename, $dirname, $filetype, $md5, $create_date, $obsolete) = $h->fetchrow_array()) {
 769         if (!$obsolete) {
 770             push @$file_info, {
 771                 file_id => $file_id,
 772                 basename => $basename,
 773                 dirname  => $dirname,
 774                 file_type => $filetype,
 775                 md5checksum => $md5,
 776                 create_date => $create_date
 777             };
 778         }
 779         else {
 780             push @$deleted_file_info, {
 781                 file_id => $file_id,
 782                 basename => $basename,
 783                 dirname  => $dirname,
 784                 file_type => $filetype,
 785                 md5checksum => $md5,
 786                 create_date => $create_date
 787             };
 788         }
 789     }
 790
 791     my $data = {
 792         files => $file_info,
 793         deleted_files => $deleted_file_info
 794     };
 795     return $data;
 796 }
 797
 798
 799 sub manage_genotyping : Path("/breeders/genotyping") Args(0) {
 800     my $self = shift;
 801     my $c = shift;
 802
 803     if (!$c->user()) {
 804         # redirect to login page
 805         $c->res->redirect( uri( path => '/user/login', query => { goto_url => $c->req->uri->path_query } ) );
 806         return;
 807     }
 808
 809     my $schema = $c->dbic_schema('Bio::Chado::Schema');
 810
 811     my $projects = CXGN::BreedersToolbox::Projects->new( { schema=> $schema } );
 812
 813     my $breeding_programs = $projects->get_breeding_programs();
 814
 815     my %genotyping_trials_by_breeding_project = ();
 816
 817     foreach my $bp (@$breeding_programs) {
 818         $genotyping_trials_by_breeding_project{$bp->[1]}= $projects->get_genotyping_trials_by_breeding_program($bp->[0]);
 819     }
 820
 821     $genotyping_trials_by_breeding_project{'Other'} = $projects->get_genotyping_trials_by_breeding_program();
 822
 823     my $genotyping_facilities = $c->config->{genotyping_facilities};
 824     my @facilities = split ',',$genotyping_facilities;
 825
 826     $c->stash->{locations} = $projects->get_all_locations($c);
 827
 828     $c->stash->{genotyping_trials_by_breeding_project} = \%genotyping_trials_by_breeding_project;
 829
 830     $c->stash->{breeding_programs} = $breeding_programs;
 831
 832     $c->stash->{facilities} = \@facilities;
 833
 834     $c->stash->{template} = '/breeders_toolbox/manage_genotyping.mas';
 835 }
 836
 837 sub manage_genotype_qc : Path("/breeders/genotype_qc") :Args(0) {
 838     my $self = shift;
 839     my $c = shift;
 840
 841     if (!$c->user()) {
 842         # redirect to login page
 843         $c->res->redirect( uri( path => '/user/login', query => { goto_url => $c->req->uri->path_query } ) );
 844         return;
 845     }
 846
 847     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 848
 849     $c->stash->{template} = '/breeders_toolbox/manage_genotype_qc.mas';
 850 }
 851
 852
 853 sub manage_markers : Path("/breeders/markers") Args(0) {
 854     my $self = shift;
 855     my $c = shift;
 856
 857     $c->stash->{template} = '/breeders_toolbox/markers/manage_markers.mas';
 858 }
 859
 860 sub manage_drone_imagery : Path("/breeders/drone_imagery") Args(0) {
 861     my $self = shift;
 862     my $c = shift;
 863
 864     if (!$c->user()) {
 865         # redirect to login page
 866         $c->res->redirect( uri( path => '/user/login', query => { goto_url => $c->req->uri->path_query } ) );
 867         return;
 868     }
 869
 870     my $schema = $c->dbic_schema('Bio::Chado::Schema');
 871     $c->stash->{template} = '/breeders_toolbox/manage_drone_imagery.mas';
 872 }
 873
 874 1;