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
  24
  25 BEGIN { extends 'Catalyst::Controller'; }
  26
  27 sub manage_breeding_programs : Path("/breeders/manage_programs") :Args(0) {
  28     my $self = shift;
  29     my $c = shift;
  30
  31     if (!$c->user()) {
  32
  33         # redirect to login page
  34         $c->res->redirect( uri( path => '/solpeople/login.pl', query => { goto_url => $c->req->uri->path_query } ) );
  35         return;
  36     }
  37
  38     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
  39
  40     my $projects = CXGN::BreedersToolbox::Projects->new( { schema=> $schema } );
  41
  42     my $breeding_programs = $projects->get_breeding_programs();
  43
  44     $c->stash->{breeding_programs} = $breeding_programs;
  45     $c->stash->{user} = $c->user();
  46
  47     $c->stash->{template} = '/breeders_toolbox/breeding_programs.mas';
  48
  49
  50 }
  51
  52 sub manage_trials : Path("/breeders/trials") Args(0) {
  53     my $self = shift;
  54     my $c = shift;
  55
  56     if (!$c->user()) {
  57
  58         # redirect to login page
  59         $c->res->redirect( uri( path => '/solpeople/login.pl', query => { goto_url => $c->req->uri->path_query } ) );
  60         return;
  61     }
  62
  63     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
  64
  65     my $projects = CXGN::BreedersToolbox::Projects->new( { schema=> $schema } );
  66
  67     my $breeding_programs = $projects->get_breeding_programs();
  68
  69     # use get_all_locations, as other calls for locations can be slow
  70     #
  71     $c->stash->{locations} = $projects->get_all_locations();
  72
  73     $c->stash->{breeding_programs} = $breeding_programs;
  74
  75     $c->stash->{template} = '/breeders_toolbox/manage_projects.mas';
  76 }
  77
  78 sub manage_accessions : Path("/breeders/accessions") Args(0) {
  79     my $self = shift;
  80     my $c = shift;
  81     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
  82     my $list_id = $c->req->param('list_id') || ''; #If a list_id is given in the URL, then the add accessions process will automatically begin with that list.
  83
  84     if (!$c->user()) {
  85         # redirect to login page
  86         #
  87         $c->res->redirect( uri( path => '/solpeople/login.pl', query => { goto_url => $c->req->uri->path_query } ) );
  88         return;
  89     }
  90
  91     my $ac = CXGN::BreedersToolbox::Accessions->new( { schema=>$schema });
  92
  93     my $accessions = $ac->get_all_accessions($c);
  94     # my $populations = $ac->get_all_populations($c);
  95
  96     my @editable_stock_props = split ',', $c->config->{editable_stock_props};
  97     my %editable_stock_props = map { $_=>1 } @editable_stock_props;
  98
  99     $c->stash->{accessions} = $accessions;
 100     $c->stash->{list_id} = $list_id;
 101     #$c->stash->{population_groups} = $populations;
 102     $c->stash->{preferred_species} = $c->config->{preferred_species};
 103     $c->stash->{editable_stock_props} = \%editable_stock_props;
 104     $c->stash->{template} = '/breeders_toolbox/manage_accessions.mas';
 105 }
 106
 107 sub manage_roles : Path("/breeders/manage_roles") Args(0) {
 108     my $self = shift;
 109     my $c = shift;
 110
 111     if (!$c->user()) {
 112         $c->res->redirect( uri( path => '/solpeople/login.pl', query => { goto_url => $c->req->uri->path_query } ) );
 113         return;
 114     }
 115
 116     $c->stash->{is_curator} = $c->user->check_roles("curator");
 117
 118     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 119     my $person_roles = CXGN::People::Roles->new({ bcs_schema=>$schema });
 120     my $breeding_programs = $person_roles->get_breeding_program_roles();
 121
 122     $c->stash->{roles} = $breeding_programs;
 123     $c->stash->{template} = '/breeders_toolbox/manage_roles.mas';
 124 }
 125
 126
 127 sub manage_locations : Path("/breeders/locations") Args(0) {
 128     my $self = shift;
 129     my $c = shift;
 130
 131     if (!$c->user()) {
 132
 133         # redirect to login page
 134         #
 135         $c->res->redirect( uri( path => '/solpeople/login.pl', query => { goto_url => $c->req->uri->path_query } ) );
 136         return;
 137     }
 138
 139     $c->assets->include('/static/css/leaflet.css');
 140     $c->assets->include('/static/css/leaflet.extra-markers.min.css');
 141     $c->assets->include('/static/css/esri-leaflet-geocoder.css');
 142
 143     $c->stash->{user_id} = $c->user()->get_object()->get_sp_person_id();
 144
 145     $c->stash->{template} = '/breeders_toolbox/manage_locations.mas';
 146 }
 147
 148 sub manage_nurseries : Path("/breeders/nurseries") Args(0) {
 149     my $self = shift;
 150     my $c = shift;
 151
 152     if (!$c->user()) {
 153
 154         # redirect to login page
 155         #
 156         $c->res->redirect( uri( path => '/solpeople/login.pl', query => { goto_url => $c->req->uri->path_query } ) );
 157         return;
 158     }
 159     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 160     my $bp = CXGN::BreedersToolbox::Projects->new( { schema=>$schema });
 161     my $breeding_programs = $bp->get_breeding_programs();
 162
 163     $c->stash->{user_id} = $c->user()->get_object()->get_sp_person_id();
 164
 165     $c->stash->{locations} = $bp->get_all_locations($c);
 166
 167     #$c->stash->{projects} = $self->get_projects($c);
 168
 169     $c->stash->{programs} = $breeding_programs;
 170
 171     $c->stash->{roles} = $c->user()->roles();
 172
 173     $c->stash->{nurseries} = $self->get_nurseries($c);
 174
 175     $c->stash->{template} = '/breeders_toolbox/manage_nurseries.mas';
 176
 177 }
 178
 179 sub manage_crosses : Path("/breeders/crosses") Args(0) {
 180     my $self = shift;
 181     my $c = shift;
 182
 183     if (!$c->user()) {
 184
 185         # redirect to login page
 186         #
 187         $c->res->redirect( uri( path => '/solpeople/login.pl', query => { goto_url => $c->req->uri->path_query } ) );
 188         return;
 189     }
 190     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 191     my $bp = CXGN::BreedersToolbox::Projects->new( { schema=>$schema });
 192     my $breeding_programs = $bp->get_breeding_programs();
 193
 194     my $crossingtrial = CXGN::BreedersToolbox::Projects->new( { schema=>$schema });
 195     my $crossing_trials = $crossingtrial->get_crossing_trials();
 196
 197     $c->stash->{user_id} = $c->user()->get_object()->get_sp_person_id();
 198
 199     $c->stash->{locations} = $bp->get_all_locations($c);
 200
 201     $c->stash->{programs} = $breeding_programs;
 202
 203     $c->stash->{crossing_trials} = $crossing_trials;
 204
 205     $c->stash->{roles} = $c->user()->roles();
 206
 207     $c->stash->{cross_populations} = $self->get_crosses($c);
 208
 209     $c->stash->{template} = '/breeders_toolbox/manage_crosses.mas';
 210
 211 }
 212
 213 sub manage_phenotyping :Path("/breeders/phenotyping") Args(0) {
 214     my $self =shift;
 215     my $c = shift;
 216
 217     if (!$c->user()) {
 218         $c->res->redirect( uri( path => '/solpeople/login.pl', query => { goto_url => $c->req->uri->path_query } ) );
 219         return;
 220     }
 221
 222     my $data = $self->get_phenotyping_data($c);
 223
 224     $c->stash->{phenotype_files} = $data->{phenotype_files};
 225     $c->stash->{deleted_phenotype_files} = $data->{deleted_phenotype_files};
 226
 227     $c->stash->{template} = '/breeders_toolbox/manage_phenotyping.mas';
 228
 229 }
 230
 231 sub manage_upload :Path("/breeders/upload") Args(0) {
 232     my $self =shift;
 233     my $c = shift;
 234     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 235
 236     if (!$c->user()) {
 237         $c->res->redirect( uri( path => '/solpeople/login.pl', query => { goto_url => $c->req->uri->path_query } ) );
 238         return;
 239     }
 240
 241     my $projects = CXGN::BreedersToolbox::Projects->new( { schema=> $schema } );
 242     my $breeding_programs = $projects->get_breeding_programs();
 243     $c->stash->{locations} = $projects->get_all_locations();
 244     $c->stash->{breeding_programs} = $breeding_programs;
 245     $c->stash->{timestamp} = localtime;
 246     $c->stash->{preferred_species} = $c->config->{preferred_species};
 247     $c->stash->{template} = '/breeders_toolbox/manage_upload.mas';
 248 }
 249
 250 sub manage_plot_phenotyping :Path("/breeders/plot_phenotyping") Args(0) {
 251     my $self =shift;
 252     my $c = shift;
 253     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 254     my $stock_id = $c->req->param('stock_id');
 255
 256     if (!$c->user()) {
 257              $c->res->redirect( uri( path => '/solpeople/login.pl', query => { goto_url => $c->req->uri->path_query } ) );
 258               return;
 259     }
 260     my $stock = $schema->resultset("Stock::Stock")->find( { stock_id=>$stock_id })->uniquename();
 261
 262     $c->stash->{plot_name} = $stock;
 263     $c->stash->{stock_id} = $stock_id;
 264     $c->stash->{template} = '/breeders_toolbox/manage_plot_phenotyping.mas';
 265
 266 }
 267
 268 sub manage_trial_phenotyping :Path("/breeders/trial_phenotyping") Args(0) {
 269     my $self =shift;
 270     my $c = shift;
 271     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 272     my $trial_id = $c->req->param('trial_id');
 273
 274     if (!$c->user()) {
 275              $c->res->redirect( uri( path => '/solpeople/login.pl', query => { goto_url => $c->req->uri->path_query } ) );
 276               return;
 277     }
 278     my $project_name = $schema->resultset("Project::Project")->find( { project_id=>$trial_id })->name();
 279
 280     $c->stash->{trial_name} = $project_name;
 281     $c->stash->{trial_id} = $trial_id;
 282     $c->stash->{template} = '/breeders_toolbox/manage_trial_phenotyping.mas';
 283 }
 284
 285 sub manage_odk_data_collection :Path("/breeders/odk") Args(0) {
 286     my $self =shift;
 287     my $c = shift;
 288     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 289
 290     if (!$c->user()) {
 291         $c->res->redirect( uri( path => '/solpeople/login.pl', query => { goto_url => $c->req->uri->path_query } ) );
 292         return;
 293     }
 294     $c->stash->{odk_crossing_data_service_name} = $c->config->{odk_crossing_data_service_name};
 295     $c->stash->{odk_crossing_data_service_url} = $c->config->{odk_crossing_data_service_url};
 296     $c->stash->{odk_crossing_data_form_name} = $c->config->{odk_crossing_data_form_name};
 297     $c->stash->{odk_crossing_data_test_form_name} = $c->config->{odk_crossing_data_test_form_name};
 298     $c->stash->{odk_phenotyping_data_service_name} = $c->config->{odk_phenotyping_data_service_name};
 299     $c->stash->{odk_phenotyping_data_service_url} = $c->config->{odk_phenotyping_data_service_url};
 300     $c->stash->{template} = '/breeders_toolbox/manage_odk_data_collection.mas';
 301 }
 302
 303 sub manage_phenotyping_download : Path("/breeders/phenotyping/download") Args(1) {
 304     my $self =shift;
 305     my $c = shift;
 306     my $file_id = shift;
 307
 308     my $metadata_schema = $c->dbic_schema('CXGN::Metadata::Schema');
 309     my $file_row = $metadata_schema->resultset("MdFiles")->find({file_id => $file_id});
 310     my $file_destination =  catfile($file_row->dirname, $file_row->basename);
 311     #print STDERR "\n\n\nfile name:".$file_row->basename."\n";
 312     my $contents = read_file($file_destination);
 313     my $file_name = $file_row->basename;
 314     $c->res->content_type('Application/trt');
 315     $c->res->header('Content-Disposition', qq[attachment; filename="$file_name"]);
 316     $c->res->body($contents);
 317 }
 318
 319 sub manage_phenotyping_view : Path("/breeders/phenotyping/view") Args(1) {
 320     my $self =shift;
 321     my $c = shift;
 322     my $file_id = shift;
 323
 324     my $metadata_schema = $c->dbic_schema('CXGN::Metadata::Schema');
 325     my $file_row = $metadata_schema->resultset("MdFiles")->find({file_id => $file_id});
 326     my $file_destination =  catfile($file_row->dirname, $file_row->basename);
 327     #print STDERR "\n\n\nfile name:".$file_row->basename."\n";
 328     my @contents = ReadData ($file_destination);
 329     #print STDERR Dumper \@contents;
 330     my $file_name = $file_row->basename;
 331     $c->stash->{file_content} = \@contents;
 332     $c->stash->{filename} = $file_name;
 333     $c->stash->{template} = '/breeders_toolbox/view_file.mas';
 334 }
 335
 336 sub make_cross_form :Path("/stock/cross/new") :Args(0) {
 337     my ($self, $c) = @_;
 338     $c->stash->{template} = '/breeders_toolbox/new_cross.mas';
 339     if ($c->user()) {
 340       my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 341       # get projects
 342       my @rows = $schema->resultset('Project::Project')->all();
 343       my @projects = ();
 344       foreach my $row (@rows) {
 345         push @projects, [ $row->project_id, $row->name, $row->description ];
 346       }
 347       $c->stash->{project_list} = \@projects;
 348       @rows = $schema->resultset('NaturalDiversity::NdGeolocation')->all();
 349       my @locations = ();
 350       foreach my $row (@rows) {
 351         push @locations,  [ $row->nd_geolocation_id,$row->description ];
 352       }
 353       $c->stash->{locations} = \@locations;
 354
 355     }
 356     else {
 357       $c->res->redirect( uri( path => '/solpeople/login.pl', query => { goto_url => $c->req->uri->path_query } ) );
 358       return;
 359     }
 360 }
 361
 362
 363 sub make_cross :Path("/stock/cross/generate") :Args(0) {
 364     my ($self, $c) = @_;
 365     $c->stash->{template} = '/breeders_toolbox/progeny_from_crosses.mas';
 366     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 367     my $cross_name = $c->req->param('cross_name');
 368     $c->stash->{cross_name} = $cross_name;
 369     my $trial_id = $c->req->param('trial_id');
 370     $c->stash->{trial_id} = $trial_id;
 371     #my $location = $c->req->param('location_id');
 372     my $maternal = $c->req->param('maternal');
 373     my $paternal = $c->req->param('paternal');
 374     my $prefix = $c->req->param('prefix');
 375     my $suffix = $c->req->param('suffix');
 376     my $progeny_number = $c->req->param('progeny_number');
 377     my $visible_to_role = $c->req->param('visible_to_role');
 378
 379     if (! $c->user()) { # redirect
 380         $c->res->redirect( uri( path => '/solpeople/login.pl', query => { goto_url => $c->req->uri->path_query } ) );
 381         return;
 382     }
 383
 384
 385     #check that progeny number is an integer less than maximum allowed
 386     my $maximum_progeny_number = 1000;
 387     if ((! $progeny_number =~ m/^\d+$/) or ($progeny_number > $maximum_progeny_number)){
 388       #redirect to error page?
 389       return;
 390     }
 391
 392     #check that parent names are not blank
 393     if ($maternal eq "" or $paternal eq "") {
 394       return;
 395     }
 396
 397     #check that parents exist in the database
 398     if (! $schema->resultset("Stock::Stock")->find({name=>$maternal,})){
 399       return;
 400     }
 401     if (! $schema->resultset("Stock::Stock")->find({name=>$paternal,})){
 402       return;
 403     }
 404
 405     #check that cross name does not already exist
 406     if ($schema->resultset("Stock::Stock")->find({name=>$cross_name})){
 407       return;
 408     }
 409
 410     #check that progeny do not already exist
 411     if ($schema->resultset("Stock::Stock")->find({name=>$prefix.$cross_name.$suffix."-1",})){
 412       return;
 413     }
 414
 415     my $organism = $schema->resultset("Organism::Organism")->find_or_create(
 416     {
 417         genus   => 'Manihot',
 418         species => 'Manihot esculenta',
 419     } );
 420     my $organism_id = $organism->organism_id();
 421
 422     my $accession_cvterm = SGN::Model::Cvterm->get_cvterm_row($schema, 'accession', 'stock_type');
 423
 424     my $population_cvterm = $schema->resultset("Cv::Cvterm")->find(
 425       { name   => 'population',
 426     });
 427
 428
 429     my $female_parent_stock = $schema->resultset("Stock::Stock")->find(
 430         { name       => $maternal,
 431         } );
 432
 433     my $male_parent_stock = $schema->resultset("Stock::Stock")->find(
 434             { name       => $paternal,
 435             } );
 436
 437     my $population_stock = $schema->resultset("Stock::Stock")->find_or_create(
 438             { organism_id => $organism_id,
 439               name       => $cross_name,
 440               uniquename => $cross_name,
 441               type_id => $population_cvterm->cvterm_id,
 442             } );
 443       my $female_parent =  SGN::Model::Cvterm->get_cvterm_row($schema, 'female_parent',  'stock_relationship');
 444
 445       my $male_parent =  SGN::Model::Cvterm->get_cvterm_row($schema, 'male_parent', 'stock_relationship');
 446
 447
 448       my $population_members =  SGN::Model::Cvterm->get_cvterm_row($schema,  'cross_relationship','stock_relationship');
 449
 450
 451     my $visible_to_role_cvterm =  SGN::Model::Cvterm->get_cvterm_row($schema,  'visible_to_role', 'local');
 452
 453     my $increment = 1;
 454     while ($increment < $progeny_number + 1) {
 455         $increment = sprintf "%03d", $increment;
 456         my $stock_name = $prefix.$cross_name."_".$increment.$suffix;
 457       my $accession_stock = $schema->resultset("Stock::Stock")->create(
 458             { organism_id => $organism_id,
 459               name       => $stock_name,
 460               uniquename => $stock_name,
 461               type_id     => $accession_cvterm->cvterm_id,
 462             } );
 463       $accession_stock->find_or_create_related('stock_relationship_objects', {
 464                 type_id => $female_parent->cvterm_id(),
 465                 object_id => $accession_stock->stock_id(),
 466                 subject_id => $female_parent_stock->stock_id(),
 467                                                   } );
 468       $accession_stock->find_or_create_related('stock_relationship_objects', {
 469                 type_id => $male_parent->cvterm_id(),
 470                 object_id => $accession_stock->stock_id(),
 471                 subject_id => $male_parent_stock->stock_id(),
 472                                                   } );
 473       $accession_stock->find_or_create_related('stock_relationship_objects', {
 474                 type_id => $population_members->cvterm_id(),
 475                 object_id => $accession_stock->stock_id(),
 476                 subject_id => $population_stock->stock_id(),
 477                                                   } );
 478       if ($visible_to_role ne "") {
 479         my $accession_stock_prop = $schema->resultset("Stock::Stockprop")->find_or_create(
 480                { type_id =>$visible_to_role_cvterm->cvterm_id(),
 481                  value => $visible_to_role,
 482                  stock_id => $accession_stock->stock_id()
 483                  });
 484       }
 485       $increment++;
 486
 487     }
 488     if ($@) {
 489     }
 490 }
 491
 492 sub selection_index : Path("/selection/index") :Args(0) {
 493     my $self = shift;
 494     my $c = shift;
 495
 496     if (!$c->user()) {
 497
 498         # redirect to login page
 499         $c->res->redirect( uri( path => '/solpeople/login.pl', query => { goto_url => $c->req->uri->path_query } ) );
 500         return;
 501     }
 502
 503 #    my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 504
 505   #  my $projects = CXGN::BreedersToolbox::Projects->new( { schema=> $schema } );
 506
 507 #    my $breeding_programs = $projects->get_breeding_programs();
 508
 509   #  $c->stash->{breeding_programs} = $breeding_programs;
 510     $c->stash->{user} = $c->user();
 511
 512     $c->stash->{template} = '/breeders_toolbox/selection_index.mas';
 513
 514
 515 }
 516
 517
 518 sub breeder_home :Path("/breeders/home") Args(0) {
 519     my ($self , $c) = @_;
 520
 521
 522     if (!$c->user()) {
 523
 524         # redirect to login page
 525         $c->res->redirect( uri( path => '/solpeople/login.pl', query => { goto_url => $c->req->uri->path_query } ) );
 526         return;
 527     }
 528
 529     # my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 530     # my $bp = CXGN::BreedersToolbox::Projects->new( { schema=>$schema });
 531     # my $breeding_programs = $bp->get_breeding_programs();
 532
 533     # $c->stash->{programs} = $breeding_programs;
 534     # $c->stash->{breeding_programs} = $breeding_programs;
 535
 536     # # my $locations_by_breeding_program;
 537     # # foreach my $b (@$breeding_programs) {
 538     # #     $locations_by_breeding_program->{$b->[1]} = $bp->get_locations_by_breeding_program($b->[0]);
 539     # # }
 540     # # $locations_by_breeding_program->{'Other'} = $bp->get_locations_by_breeding_program();
 541
 542     # $c->stash->{locations_by_breeding_program} = ""; #$locations_by_breeding_program;
 543
 544     # # get roles
 545     # #
 546     # my @roles = $c->user->roles();
 547     # $c->stash->{roles}=\@roles;
 548
 549     # $c->stash->{cross_populations} = $self->get_crosses($c);
 550
 551     # $c->stash->{stockrelationships} = $self->get_stock_relationships($c);
 552
 553     # my $locations = $bp->get_locations($c);
 554
 555     # $c->stash->{locations} = $locations;
 556     # # get uploaded phenotype files
 557     # #
 558
 559     # my $data = $self->get_phenotyping_data($c);
 560
 561     # $c->stash->{phenotype_files} = $data->{file_info};
 562     # $c->stash->{deleted_phenotype_files} = $data->{deleted_file_info};
 563
 564
 565     $c->stash->{template} = '/breeders_toolbox/home.mas';
 566 }
 567
 568
 569 sub breeder_search : Path('/breeders/search/') :Args(0) {
 570     my ($self, $c) = @_;
 571     $c->stash->{dataset_id} = $c->req->param('dataset_id');
 572     $c->stash->{template} = '/breeders_toolbox/breeder_search_page.mas';
 573
 574 }
 575
 576
 577 sub get_crosses : Private {
 578     my $self = shift;
 579     my $c = shift;
 580
 581     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 582
 583     # get crosses
 584     #
 585     my $stock_type_cv = $schema->resultset("Cv::Cv")->find( {name=>'stock_type'});
 586     my $cross_cvterm = $schema->resultset("Cv::Cvterm")->find(
 587         { name   => 'cross',
 588           cv_id => $stock_type_cv->cv_id(),
 589         });
 590     my @cross_populations = ();
 591
 592     if ($cross_cvterm) {
 593
 594       my @cross_population_stocks = $schema->resultset("Stock::Stock")->search(
 595                                                                                { type_id => $cross_cvterm->cvterm_id, is_obsolete => 'f'
 596                                                                                } );
 597       foreach my $cross_pop (@cross_population_stocks) {
 598         push @cross_populations, [$cross_pop->name,$cross_pop->stock_id];
 599       }
 600     }
 601     return  \@cross_populations;
 602 }
 603
 604
 605
 606 sub get_phenotyping_data : Private {
 607     my $self = shift;
 608     my $c = shift;
 609
 610     my $metadata_schema = $c->dbic_schema("CXGN::Metadata::Schema");
 611
 612     my $file_info = [];
 613     my $deleted_file_info = [];
 614
 615      my $metadata_rs = $metadata_schema->resultset("MdMetadata")->search( { create_person_id => $c->user()->get_object->get_sp_person_id() }, { order_by => 'create_date' } );
 616
 617     print STDERR "RETRIEVED ".$metadata_rs->count()." METADATA ENTRIES...\n";
 618
 619     while (my $md_row = ($metadata_rs->next())) {
 620         my $file_rs = $metadata_schema->resultset("MdFiles")->search( { metadata_id => $md_row->metadata_id(), filetype => {'!=' => 'document_browser'} } );
 621
 622         if (!$md_row->obsolete) {
 623             while (my $file_row = $file_rs->next()) {
 624                 push @$file_info, { file_id => $file_row->file_id(),
 625                                     basename => $file_row->basename,
 626                                     dirname  => $file_row->dirname,
 627                                     file_type => $file_row->filetype,
 628                                     md5checksum => $file_row->md5checksum,
 629                                     create_date => $md_row->create_date,
 630                 };
 631             }
 632         }
 633         else {
 634             while (my $file_row = $file_rs->next()) {
 635                 push @$deleted_file_info, { file_id => $file_row->file_id(),
 636                                             basename => $file_row->basename,
 637                                             dirname => $file_row->dirname,
 638                                             file_type => $file_row->filetype,
 639                                             md5checksum => $file_row->md5checksum,
 640                                             create_date => $md_row->create_date,
 641                 };
 642             }
 643         }
 644     }
 645
 646     my $data = { phenotype_files => $file_info,
 647                  deleted_phenotype_files => $deleted_file_info,
 648     };
 649     return $data;
 650
 651
 652 }
 653
 654 sub manage_genotyping : Path("/breeders/genotyping") Args(0) {
 655     my $self = shift;
 656     my $c = shift;
 657
 658     if (!$c->user()) {
 659         # redirect to login page
 660         $c->res->redirect( uri( path => '/solpeople/login.pl', query => { goto_url => $c->req->uri->path_query } ) );
 661         return;
 662     }
 663
 664     my $schema = $c->dbic_schema('Bio::Chado::Schema');
 665
 666     my $projects = CXGN::BreedersToolbox::Projects->new( { schema=> $schema } );
 667
 668     my $breeding_programs = $projects->get_breeding_programs();
 669
 670     my %genotyping_trials_by_breeding_project = ();
 671
 672     foreach my $bp (@$breeding_programs) {
 673         $genotyping_trials_by_breeding_project{$bp->[1]}= $projects->get_genotyping_trials_by_breeding_program($bp->[0]);
 674     }
 675
 676     $genotyping_trials_by_breeding_project{'Other'} = $projects->get_genotyping_trials_by_breeding_program();
 677
 678     $c->stash->{locations} = $projects->get_all_locations($c);
 679
 680     $c->stash->{genotyping_trials_by_breeding_project} = \%genotyping_trials_by_breeding_project;
 681
 682     $c->stash->{breeding_programs} = $breeding_programs;
 683
 684     $c->stash->{template} = '/breeders_toolbox/manage_genotyping.mas';
 685 }
 686
 687
 688 1;