lib/CXGN/Trial/Folder.pm

   1
   2 package CXGN::Trial::Folder;
   3
   4 use CXGN::Chado::Cvterm;
   5 use CXGN::Location;
   6 use Moose;
   7 use SGN::Model::Cvterm;
   8 use Data::Dumper;
   9 use JSON;
  10
  11 has 'bcs_schema' => ( isa => 'Bio::Chado::Schema',
  12         is => 'rw',
  13         required => 1,
  14 );
  15
  16 has 'folder_id' => (isa => "Int",
  17         is => 'rw',
  18 );
  19
  20 has 'children' => (is => 'rw',
  21         lazy => 1,
  22         default => sub {
  23                 my $self = shift;
  24                 $self->_get_children();
  25         }
  26 );
  27
  28 has 'is_folder' => (isa => 'Bool',
  29         is => 'rw',
  30         default => 0,
  31 );
  32
  33 has 'folder_type' => (isa => 'Str',
  34         is => 'rw',
  35 );
  36
  37 has 'name' => (isa => 'Str',
  38         is => 'rw',
  39         default => 'Untitled',
  40 );
  41
  42 has 'description' => (
  43         isa => 'Str',
  44         is  => 'rw'
  45 );
  46
  47 has 'folder_for_trials' => (isa => 'Bool',
  48         is => 'rw',
  49         default => 0,
  50 );
  51
  52 has 'folder_for_crosses' => (isa => 'Bool',
  53         is => 'rw',
  54         default => 0,
  55 );
  56
  57 has 'folder_for_genotyping_trials' => (isa => 'Bool',
  58         is => 'rw',
  59         default => 0,
  60 );
  61
  62 has 'folder_for_genotyping_projects' => (isa => 'Bool',
  63         is => 'rw',
  64         default => 0,
  65 );
  66
  67 has 'folder_for_tracking_activities' => (isa => 'Bool',
  68         is => 'rw',
  69         default => 0,
  70 );
  71
  72 has 'folder_for_transformations' => (isa => 'Bool',
  73         is => 'rw',
  74         default => 0,
  75 );
  76
  77 has 'location_id' => (isa => 'Int',
  78         is => 'rw',
  79 );
  80
  81 has 'location_name' => (isa => 'Str',
  82         is => 'rw',
  83 );
  84
  85 has 'breeding_program_trial_relationship_id' =>  (isa => 'Int',
  86         is => 'rw',
  87 );
  88
  89 has 'project_parent' => (isa => 'Bio::Chado::Schema::Result::Project::Project',
  90         is => 'rw',
  91 );
  92
  93 has 'breeding_program' => (isa => 'Bio::Chado::Schema::Result::Project::Project',
  94         is => 'rw',
  95 );
  96
  97 has 'breeding_program_cvterm_id' => (isa => 'Int',
  98         is => 'rw',
  99 );
 100
 101 has 'folder_cvterm_id' => (isa => 'Int',
 102         is => 'rw',
 103 );
 104
 105 has 'additional_info' => (
 106         is  => 'rw'
 107 );
 108
 109 sub BUILD {
 110         my $self = shift;
 111
 112         my $row = $self->bcs_schema()->resultset('Project::Project')->find( { project_id=>$self->folder_id() });
 113
 114         if (!$row) {
 115                 die "The specified folder with id ".$self->folder_id()." does not exist!";
 116         }
 117
 118         $self->name($row->name());
 119         $self->description($row->description());
 120
 121         my $breeding_program_type_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema,'breeding_program', 'project_property')->cvterm_id();
 122         my $folder_for_trials_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema, 'folder_for_trials', 'project_property')->cvterm_id();
 123         my $folder_for_crosses_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema, 'folder_for_crosses', 'project_property')->cvterm_id();
 124         my $folder_for_genotyping_trials_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema, 'folder_for_genotyping_trials', 'project_property')->cvterm_id();
 125         my $folder_for_genotyping_projects_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema, 'folder_for_genotyping_projects', 'project_property')->cvterm_id();
 126         my $folder_for_tracking_activities_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema, 'folder_for_tracking_activities', 'project_property')->cvterm_id();
 127         my $folder_for_transformations_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema, 'folder_for_transformations', 'project_property')->cvterm_id();
 128         my $folder_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema,'trial_folder', 'project_property')->cvterm_id();
 129         my $analyses_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema,'analysis_metadata_json', 'project_property')->cvterm_id();
 130         my $breeding_program_trial_relationship_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema,'breeding_program_trial_relationship', 'project_relationship')->cvterm_id();
 131         my $additional_info_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema,'project_additional_info', 'project_property')->cvterm_id();
 132
 133         $self->breeding_program_cvterm_id($breeding_program_type_id);
 134         $self->folder_cvterm_id($folder_cvterm_id);
 135         $self->breeding_program_trial_relationship_id($breeding_program_trial_relationship_id);
 136
 137         my $folder_type = $self->bcs_schema()->resultset('Project::Projectprop')-> search( { project_id => $self->folder_id() });
 138         while (my $folder_type_row = $folder_type->next) {
 139                 if ($folder_type_row->type_id() == $self->folder_cvterm_id() ) {
 140                         $self->folder_type("folder");
 141                         $self->is_folder(1);
 142                 } elsif ($folder_type_row->type_id() == $self->breeding_program_cvterm_id()) {
 143                         $self->folder_type("breeding_program");
 144                         $self->breeding_program($row);
 145                 } elsif ($folder_type_row->type_id() == $folder_for_trials_cvterm_id) {
 146                         $self->folder_for_trials(1);
 147                 } elsif ($folder_type_row->type_id() == $folder_for_crosses_cvterm_id) {
 148                         $self->folder_for_crosses(1);
 149                 } elsif ($folder_type_row->type_id() == $folder_for_genotyping_trials_cvterm_id) {
 150                         $self->folder_for_genotyping_trials(1);
 151                 } elsif ($folder_type_row->type_id() == $folder_for_genotyping_projects_cvterm_id) {
 152                         $self->folder_for_genotyping_projects(1);
 153                 } elsif ($folder_type_row->type_id() == $folder_for_tracking_activities_cvterm_id) {
 154                         $self->folder_for_tracking_activities(1);
 155                 } elsif ($folder_type_row->type_id() == $folder_for_transformations_cvterm_id) {
 156                         $self->folder_for_transformations(1);
 157                 } elsif ($folder_type_row->type_id() == $additional_info_cvterm_id) {
 158                         my $additional_info = decode_json($folder_type_row->value);
 159                         $self->additional_info($additional_info);
 160                 }
 161         }
 162
 163         if (!$self->folder_type) {
 164                 my $location_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema, 'project location',  'project_property')->cvterm_id;
 165
 166                 my $trial_type_rs = $self->bcs_schema->resultset("Project::Project")->search({ 'me.project_id' => $self->folder_id })->search_related('projectprops');
 167                 while (my $tt = $trial_type_rs->next()) {
 168                         if ($tt->value eq 'crossing_trial') {
 169                                 $self->folder_type("cross");
 170                         } elsif ($tt->value eq 'genotyping_plate') {
 171                                 $self->folder_type("genotyping_trial");
 172                         } elsif ($tt->value eq 'genotyping_plate') {
 173                                 $self->folder_type("genotyping_trial");
 174                         } elsif (($tt->value eq 'genotype_data_project') || ($tt->value eq 'pcr_genotype_data_project')) {
 175                 $self->folder_type("genotyping_project");
 176             } elsif ($tt->value eq 'sampling_trial') {
 177                 $self->folder_type("sampling_trial");
 178             } elsif ($tt->value eq 'activity_record') {
 179                 $self->folder_type('activity_record');
 180             } elsif ($tt->type_id == $analyses_cvterm_id) {
 181                 $self->folder_type("analyses");
 182                         } elsif ($tt->type_id == $location_cvterm_id) {
 183                                 $self->location_id($tt->value + 0);
 184                 my $location = CXGN::Location->new( { bcs_schema => $self->bcs_schema, nd_geolocation_id => $self->location_id } );
 185                 $self->location_name($location->name());
 186                         }
 187                 }
 188
 189                 if (!$self->folder_type) {
 190                         $self->folder_type("trial");
 191                 }
 192         }
 193
 194         my $breeding_program_rel_row = $self->bcs_schema()->resultset('Project::ProjectRelationship')->find( { subject_project_id => $self->folder_id(), type_id =>  $self->breeding_program_trial_relationship_id() });
 195         if ($breeding_program_rel_row) {
 196                 my $parent_row = $self->bcs_schema()->resultset('Project::Project')->find( { project_id=> $breeding_program_rel_row->object_project_id() });
 197                 $self->project_parent($parent_row);
 198                 $self->breeding_program($parent_row);
 199         }
 200
 201         my $folder_rel_row = $self->bcs_schema()->resultset('Project::ProjectRelationship')->find( { subject_project_id => $self->folder_id(), type_id =>  $self->folder_cvterm_id() });
 202         if ($folder_rel_row) {
 203                 my $parent_row = $self->bcs_schema()->resultset('Project::Project')->find( { project_id=> $folder_rel_row->object_project_id() });
 204                 $self->project_parent($parent_row);
 205         }
 206
 207 }
 208
 209 # class methods
 210
 211 sub create {
 212         my $class = shift;
 213         my $args = shift;
 214         my $schema = $args->{bcs_schema};
 215         my $folder_name = $args->{name};
 216         my $description = $args->{description} || "";
 217         my $breeding_program_id = $args->{breeding_program_id};
 218         my $parent_folder_id = $args->{parent_folder_id};
 219         my $folder_for_trials = $args->{folder_for_trials};
 220         my $folder_for_crosses = $args->{folder_for_crosses};
 221         my $folder_for_genotyping_trials = $args->{folder_for_genotyping_trials};
 222         my $folder_for_genotyping_projects = $args->{folder_for_genotyping_projects};
 223         my $folder_for_tracking_activities = $args->{folder_for_tracking_activities};
 224         my $folder_for_transformations = $args->{folder_for_transformations};
 225         my $additional_info = $args->{additional_info} || undef;
 226
 227         # check if name is already taken
 228         my $check_rs = $schema->resultset('Project::Project')->search( { name => $folder_name } );
 229         if ($check_rs->count() > 0) {
 230                 die "The name $folder_name cannot be used for a new folder because it already exists.";
 231         }
 232
 233         my $folder_cvterm = SGN::Model::Cvterm->get_cvterm_row($schema, 'trial_folder', 'project_property');
 234
 235         my $project = $schema->resultset('Project::Project')->create({
 236                 name => $folder_name,
 237                 description => $description,
 238         });
 239         $project->create_projectprops({ $folder_cvterm->name() => '1' });
 240
 241         if ($folder_for_trials) {
 242                 my $folder_type_cvterm = SGN::Model::Cvterm->get_cvterm_row($schema, 'folder_for_trials', 'project_property');
 243                 $project->create_projectprops({ $folder_type_cvterm->name() => '1' });
 244         }
 245         if ($folder_for_crosses) {
 246                 my $folder_type_cvterm = SGN::Model::Cvterm->get_cvterm_row($schema, 'folder_for_crosses', 'project_property');
 247                 $project->create_projectprops({ $folder_type_cvterm->name() => '1' });
 248         }
 249     if ($folder_for_genotyping_trials) {
 250         my $folder_type_cvterm = SGN::Model::Cvterm->get_cvterm_row($schema, 'folder_for_genotyping_trials', 'project_property');
 251         $project->create_projectprops({ $folder_type_cvterm->name() => '1' });
 252     }
 253     if ($folder_for_genotyping_projects) {
 254         my $folder_type_cvterm = SGN::Model::Cvterm->get_cvterm_row($schema, 'folder_for_genotyping_projects', 'project_property');
 255         $project->create_projectprops({ $folder_type_cvterm->name() => '1' });
 256     }
 257         if ($folder_for_tracking_activities) {
 258                 my $folder_type_cvterm = SGN::Model::Cvterm->get_cvterm_row($schema, 'folder_for_tracking_activities', 'project_property');
 259                 $project->create_projectprops({ $folder_type_cvterm->name() => '1' });
 260         }
 261         if ($folder_for_transformations) {
 262                 my $folder_type_cvterm = SGN::Model::Cvterm->get_cvterm_row($schema, 'folder_for_transformations', 'project_property');
 263                 $project->create_projectprops({ $folder_type_cvterm->name() => '1' });
 264         }
 265         if ($additional_info){
 266                 my $additional_info_cvterm = SGN::Model::Cvterm->get_cvterm_row($schema, 'project_additional_info', 'project_property');
 267                 $project->create_projectprops({ $additional_info_cvterm->name() => encode_json($additional_info) });
 268         }
 269
 270         my $folder = CXGN::Trial::Folder->new({
 271                 bcs_schema => $schema,
 272                 folder_id => $project->project_id()
 273         });
 274         $folder->associate_parent($parent_folder_id);
 275         $folder->associate_breeding_program($breeding_program_id);
 276
 277         return $folder;
 278 }
 279
 280 #CLASS function
 281 sub list {
 282         my $class = shift;
 283         my $args = shift;
 284         my $schema = $args->{bcs_schema};
 285         my $breeding_program_id = $args->{breeding_program_id};
 286         my $folder_for_trials = $args->{folder_for_trials};
 287         my $folder_for_crosses = $args->{folder_for_crosses};
 288         my $folder_for_genotyping_trials = $args->{folder_for_genotyping_trials};
 289         my $folder_for_genotyping_projects = $args->{folder_for_genotyping_projects};
 290         my $folder_for_tracking_activities = $args->{folder_for_tracking_activities};
 291         my $folder_for_transformations = $args->{folder_for_transformations};
 292         my $folder_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema,'trial_folder', 'project_property')->cvterm_id();
 293         my $breeding_program_trial_relationship_id = SGN::Model::Cvterm->get_cvterm_row($schema,'breeding_program_trial_relationship', 'project_relationship')->cvterm_id();
 294
 295         my %object_project_params;
 296         $object_project_params{'me.type_id'} = $breeding_program_trial_relationship_id;
 297         if ($breeding_program_id){
 298                 $object_project_params{'me.object_project_id'} = $breeding_program_id;
 299         }
 300
 301         my %projectprop_params;
 302         if (!$folder_for_trials && !$folder_for_crosses && !$folder_for_genotyping_trials && !$folder_for_genotyping_projects && !$folder_for_tracking_activities && !$folder_for_transformations){
 303                 $projectprop_params{'projectprops.type_id'} = $folder_cvterm_id;
 304         } elsif ($folder_for_trials){
 305                 my $folder_type_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'folder_for_trials', 'project_property')->cvterm_id();
 306                 $projectprop_params{'projectprops.type_id'} = $folder_type_cvterm_id;
 307         } elsif ($folder_for_crosses){
 308                 my $folder_type_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'folder_for_crosses', 'project_property')->cvterm_id();
 309                 $projectprop_params{'projectprops.type_id'} = $folder_type_cvterm_id;
 310     } elsif ($folder_for_genotyping_trials){
 311         my $folder_type_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'folder_for_genotyping_trials', 'project_property')->cvterm_id();
 312         $projectprop_params{'projectprops.type_id'} = $folder_type_cvterm_id;
 313         } elsif ($folder_for_genotyping_projects){
 314         my $folder_type_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'folder_for_genotyping_projects', 'project_property')->cvterm_id();
 315         $projectprop_params{'projectprops.type_id'} = $folder_type_cvterm_id;
 316     } elsif ($folder_for_tracking_activities){
 317         my $folder_type_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'folder_for_tracking_activities', 'project_property')->cvterm_id();
 318         $projectprop_params{'projectprops.type_id'} = $folder_type_cvterm_id;
 319     } elsif ($folder_for_transformations){
 320         my $folder_type_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'folder_for_transformations', 'project_property')->cvterm_id();
 321         $projectprop_params{'projectprops.type_id'} = $folder_type_cvterm_id;
 322     }
 323
 324         my $breeding_program_rel = $schema->resultset('Project::ProjectRelationship')->search(\%object_project_params)->search_related("subject_project")->search_related("projectprops", \%projectprop_params, {'+select'=>'subject_project.name', '+as'=>'name' } );
 325
 326         my @folders;
 327         while (my $row = $breeding_program_rel->next()) {
 328                 push @folders, [ $row->project_id(), $row->get_column('name') ];
 329         }
 330
 331         return @folders;
 332 }
 333
 334
 335
 336 ### OBJECT METHODS
 337
 338 # return a resultset with children of the folder
 339 #
 340 sub _get_children {
 341         my $self = shift;
 342
 343         my @children;
 344
 345     my $folder_cvterm_id = $self->folder_cvterm_id();
 346         my $rs = $self->bcs_schema()->resultset("Project::Project")->search_related( 'project_relationship_subject_projects', { object_project_id => $self->folder_id(), 'project_relationship_subject_projects.type_id' => $folder_cvterm_id }, { order_by => 'me.name' });
 347
 348         @children = map { $_->subject_project_id() } $rs->all();
 349
 350         my @child_folders;
 351         foreach my $id (@children) {
 352                 my $folder = CXGN::Trial::Folder->new({
 353                         bcs_schema=> $self->bcs_schema(),
 354                         folder_id=>$id,
 355                 });
 356
 357                 if ($self->folder_type() eq "breeding_program") {
 358                         if ($folder->project_parent()) {
 359                                 if ($folder->project_parent()->name() eq $self->name()) {
 360                                         #print STDERR "Pushing ".$folder->name().$folder->folder_type."\n";
 361                                         push @child_folders, $folder;
 362                                 }
 363                         }
 364                 } else {
 365                         #print STDERR "parent is not a breeding program... pushing ".$folder->name().$folder->folder_type."...\n";
 366                         push @child_folders, $folder;
 367                 }
 368         }
 369
 370         return \@child_folders;
 371 }
 372
 373 # return a resultset with children of the folder quickly
 374 #
 375 sub fast_children {
 376
 377         my $self = shift;
 378     my $schema = shift;
 379     my $parent_type = shift;
 380     my (@folder_contents, %children);
 381
 382     #print STDERR "Running get children for project ".$self->{'name'}." at time ".localtime()."\n";
 383
 384     if ($parent_type eq 'breeding_program') {
 385         my $rs = $schema->resultset("Project::Project")->search_related(
 386             'project_relationship_subject_projects',
 387             {   'type.name' => 'trial_folder'
 388             },
 389             {   join => 'type'
 390             });
 391         @folder_contents = map { $_->subject_project_id() } $rs->all();
 392     }
 393
 394         my $rs = $schema->resultset("Project::Project")->search_related(
 395         'project_relationship_subject_projects',
 396         {   object_project_id => $self->{'id'},
 397             subject_project_id => { 'not in' => \@folder_contents }
 398         },
 399         {   join      => { subject_project => { projectprops => 'type' } },
 400             '+select' => ['subject_project.name', 'projectprops.value', 'type.name'],
 401             '+as'     => ['project_name', 'project_value', 'project_type']
 402         }
 403      );
 404
 405     while (my $row = $rs->next) {
 406         my $name = $row->get_column('project_name');
 407         $children{$name}{'name'} = $name;
 408         $children{$name}{'id'} = $row->subject_project_id();
 409         if ($row->get_column('project_value')){
 410             $children{$name}{$row->get_column('project_value')} = 1;
 411         }
 412         if ($row->get_column('project_type')){
 413             $children{$name}{$row->get_column('project_type')} = 1;
 414         }
 415     }
 416
 417     #print STDERR "Finished running get children for project ".$self->{'name'}." at time ".localtime()."\n";  #Children are: ".Dumper(%children);
 418         return %children
 419 }
 420
 421 sub set_folder_content_type {
 422         my $self = shift;
 423         my $type = shift; #folder_for_trials or folder_for_crosses
 424         my $boolean_value = shift; #0 or 1
 425
 426         my $folder_type_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema, $type, 'project_property')->cvterm_id();
 427         my $prop = $self->bcs_schema->resultset('Project::Projectprop')->find({
 428                 project_id => $self->folder_id,
 429                 type_id => $folder_type_cvterm_id
 430         });
 431         if ($boolean_value){
 432                 if (!$prop){
 433                         my $new_prop = $self->bcs_schema->resultset('Project::Projectprop')->create({
 434                                 project_id => $self->folder_id,
 435                                 type_id => $folder_type_cvterm_id,
 436                                 value => '1'
 437                         });
 438                 }
 439         } else {
 440                 if ($prop){
 441                         $prop->delete();
 442                 }
 443         }
 444 }
 445
 446
 447
 448 sub associate_parent {
 449     my $self = shift;
 450         my $parent_id = shift;
 451
 452         my $folder_cvterm_id = $self->folder_cvterm_id();
 453         my $breeding_program_trial_relationship_id = $self->breeding_program_trial_relationship_id();
 454
 455         #If the user selects 'None' to remove the trial from the folder, then the parent_id will be passed as 0. No new parent will be created.
 456         if ($parent_id == 0) {
 457                 $self->remove_parents;
 458                 return;
 459         }
 460
 461         my $parent_row = $self->bcs_schema()->resultset("Project::Project")->find( { project_id => $parent_id } );
 462
 463         if (!$parent_row) {
 464                 print STDERR "The folder specified as parent does not exist";
 465                 return;
 466         }
 467
 468         my $parentprop_row = $self->bcs_schema()->resultset("Project::Projectprop")->find( { project_id => $parent_id,  type_id => { -in => [ $folder_cvterm_id, $breeding_program_trial_relationship_id ] } } );
 469
 470         if (!$parentprop_row) {
 471                 print STDERR "The specified parent folder is not of type folder or breeding program. Ignoring.";
 472                 return;
 473         }
 474
 475         $self->remove_parents;
 476
 477         my $project_rel_row = $self->bcs_schema()->resultset('Project::ProjectRelationship')->create({
 478                 object_project_id => $parent_id,
 479                 subject_project_id => $self->folder_id(),
 480                 type_id => $folder_cvterm_id,
 481         });
 482         $project_rel_row->insert();
 483
 484     $self->project_parent($parent_row);
 485
 486         my $parent_is_child = check_if_folder_is_child_in_tree($self->bcs_schema, $parent_id, $self->children());
 487         if ($parent_is_child) {
 488                 print STDERR 'Parent '.$parent_id.' is child in tree of folder '.$self->folder_id()."\n";
 489                 my $parent_folder = CXGN::Trial::Folder->new({
 490                         bcs_schema => $self->bcs_schema,
 491                         folder_id => $parent_id
 492                 });
 493                 $parent_folder->remove_parents;
 494         }
 495
 496 }
 497
 498 sub remove_parents {
 499         my $self = shift;
 500         #Remove any previous parents
 501         my $project_rels = $self->bcs_schema()->resultset('Project::ProjectRelationship')->search({
 502                 subject_project_id => $self->folder_id(),
 503                 type_id => $self->folder_cvterm_id()
 504         });
 505
 506         if ($project_rels->count() > 0) {
 507                 while (my $p = $project_rels->next()) {
 508                         print STDERR $p->subject_project_id." : ".$p->object_project_id." : Removing parent folder association...\n";
 509                         $p->delete();
 510                 }
 511         }
 512         return;
 513 }
 514
 515 sub check_if_folder_is_child_in_tree {
 516         my $schema = shift;
 517         my $folder_id = shift;
 518         my $children = shift;
 519         foreach (@$children) {
 520                 my $child_folder_id = $_->folder_id();
 521                 if ($child_folder_id == $folder_id) {
 522                         return 1;
 523                 } else{
 524                         #print STDERR $child_folder_id."\n";
 525                         my $child_folder = CXGN::Trial::Folder->new({
 526                                 bcs_schema => $schema,
 527                                 folder_id => $child_folder_id
 528                         });
 529                         return check_if_folder_is_child_in_tree($schema, $folder_id, $child_folder->children() );
 530                 }
 531         }
 532
 533         return;
 534 }
 535
 536 sub associate_breeding_program {
 537     my $self = shift;
 538     my $breeding_program_id = shift;
 539
 540     if (!$breeding_program_id) {
 541         print STDERR "No breeding_program_id provided. Ignoring association.\n";
 542         return;
 543     }
 544
 545     my $project_rel_row = $self->bcs_schema()->resultset('Project::ProjectRelationship')->find(
 546         { object_project_id => $breeding_program_id,
 547           subject_project_id =>  $self->folder_id(),
 548         });
 549
 550     if (! $project_rel_row) {
 551         #print STDERR "Creating folder association with breeding program id= $breeding_program_id, folder_id = ".$self->folder_id().", type_id = ".$self->breeding_program_trial_relationship_id()."\n";
 552         $project_rel_row = $self->bcs_schema()->resultset('Project::ProjectRelationship')->create(
 553             {
 554                 object_project_id => $breeding_program_id,
 555                 subject_project_id => $self->folder_id(),
 556                 type_id => $self->breeding_program_trial_relationship_id(),
 557             });
 558
 559         $project_rel_row->insert();
 560     }
 561     else {
 562         $project_rel_row->object_project_id($breeding_program_id);
 563         $project_rel_row->update();
 564     }
 565
 566     my $row = $self->bcs_schema()->resultset('Project::Project')->find( { project_id=> $project_rel_row->object_project_id() });
 567     $self->breeding_program($row);
 568
 569 }
 570
 571 sub delete_folder {
 572         my $self = shift;
 573
 574         my $children = $self->children();
 575         if (scalar(@$children) > 0) {
 576                 return;
 577         }
 578         my $delete_folder = $self->bcs_schema->resultset("Project::Project")->find({ project_id => $self->folder_id })->delete();
 579         return 1;
 580 }
 581
 582 sub rename_folder {
 583         my $self = shift;
 584         my $new_name = shift;
 585         my $folder_exists = $self->get_folder_by_name($new_name);
 586         return 0 if $folder_exists;
 587         my $update_folder = $self->bcs_schema->resultset("Project::Project")->find({ project_id => $self->folder_id });
 588         $update_folder->name($new_name );
 589         $update_folder->update();
 590         return 1;
 591 }
 592
 593 sub get_folder_by_name {
 594     my $self= shift;
 595     my $name = shift;
 596     my $exists = $self->bcs_schema->resultset("Project::Project")->search( { name => $name } );
 597     my $count = $exists->count();
 598     if ( $exists->count() > 0 ) { return 1 } else { return 0 }
 599     return;
 600 }
 601
 602 sub remove_parent {
 603
 604
 605 }
 606
 607
 608 sub remove_child {
 609
 610
 611 }
 612
 613 sub get_jstree_html {
 614     shift;
 615     my $self = shift;
 616     my $schema = shift;
 617     my $parent_type = shift;
 618     my $project_type_of_interest = shift // 'trial';
 619     #print STDERR "Running get js tree html on project ".$self->{'name'}." at time ".localtime()."\n";
 620     my ($folder_type_of_interest, $local_type_of_interest, $html);
 621
 622     if ($project_type_of_interest eq 'trial') {
 623         $local_type_of_interest = 'design'; # there is no 'trial' project prop, so using this as a proxy
 624         $folder_type_of_interest = 'folder_for_trials';
 625     }
 626     elsif ($project_type_of_interest eq 'cross') {
 627         $local_type_of_interest = 'crossing_trial';
 628         $folder_type_of_interest = 'folder_for_crosses';
 629     }
 630     elsif ($project_type_of_interest eq 'genotyping_trial') {
 631         $local_type_of_interest = 'genotyping_plate'; # in order to match projectprop value
 632         $folder_type_of_interest = 'folder_for_genotyping_trials';
 633     }
 634     elsif ($project_type_of_interest eq 'genotyping_project') {
 635         $local_type_of_interest = 'genotype_data_project';
 636         $folder_type_of_interest = 'folder_for_genotyping_projects';
 637     }
 638     elsif ($project_type_of_interest eq 'activity') {
 639         $local_type_of_interest = 'activity_record';
 640         $folder_type_of_interest = 'folder_for_tracking_activities';
 641         }
 642     elsif ($project_type_of_interest eq 'transformation') {
 643         $local_type_of_interest = 'transformation_project';
 644         $folder_type_of_interest = 'folder_for_transformations';
 645     }
 646
 647     $html .= _jstree_li_html($schema, $parent_type, $self->{'id'}, $self->{'name'});
 648     $html .= "<ul>";
 649
 650     my %children = fast_children($self, $schema, $parent_type);
 651     # print STDERR Dumper \%children;
 652     if (%children) {
 653         foreach my $child (sort keys %children) {
 654             #print STDERR "Working on child ".$children{$child}->{'name'}."\n";
 655
 656             if ($project_type_of_interest eq 'trial' && $children{$child}->{'analysis_experiment'}) {
 657                 $html .= _jstree_li_html($schema, 'analyses', $children{$child}->{'id'}, $children{$child}->{'name'})."</li>";
 658             }
 659 #            elsif ($project_type_of_interest eq 'trial' && $children{$child}->{'genotype_data_project'}) {
 660 #                $html .= _jstree_li_html($schema, 'genotyping_data_project', $children{$child}->{'id'}, $children{$child}->{'name'})."</li>";
 661 #            }
 662 #                       elsif ($project_type_of_interest eq 'trial' && $children{$child}->{'pcr_genotype_data_project'}) {
 663 #                $html .= _jstree_li_html($schema, 'pcr_genotyping_data_project', $children{$child}->{'id'}, $children{$child}->{'name'})."</li>";
 664 #            }
 665             elsif ($project_type_of_interest eq 'trial' && $children{$child}->{'sampling_trial'}) {
 666                 $html .= _jstree_li_html($schema, 'sampling_trial', $children{$child}->{'id'}, $children{$child}->{'name'})."</li>";
 667             }
 668             elsif ($project_type_of_interest eq 'genotyping_project' && $children{$child}->{'genotype_data_project'}) {
 669                 $html .= _jstree_li_html($schema, 'genotyping_project', $children{$child}->{'id'}, $children{$child}->{'name'})."</li>";
 670             }
 671             elsif ($project_type_of_interest eq 'genotyping_project' && $children{$child}->{'pcr_genotype_data_project'}) {
 672                 $html .= _jstree_li_html($schema, 'genotyping_project', $children{$child}->{'id'}, $children{$child}->{'name'})."</li>";
 673             }
 674             elsif ($children{$child}->{$folder_type_of_interest}) {
 675                 $html .= get_jstree_html('shift', $children{$child}, $schema, 'folder', $project_type_of_interest);
 676             }
 677             elsif (!$children{$child}->{'folder_for_crosses'} && !$children{$child}->{'folder_for_genotyping_trials'} && !$children{$child}->{'folder_for_trials'} && !$children{$child}->{'folder_for_genotyping_projects'} && !$children{$child}->{'folder_for_tracking_activities'} && !$children{$child}->{'folder_for_transformations'} && $children{$child}->{'trial_folder'}) {
 678                 $html .= get_jstree_html('shift', $children{$child}, $schema, 'folder', $project_type_of_interest);
 679             }
 680             elsif (($local_type_of_interest eq 'design' && $children{$child}->{'genotyping_plate'}) || ($local_type_of_interest eq 'design' && $children{$child}->{'genotype_data_project'}) || ($local_type_of_interest eq 'design' && $children{$child}->{'pcr_genotype_data_project'})){
 681                 next; #skip genotyping plates in field trial tree
 682             }
 683             elsif ($children{$child}->{$local_type_of_interest}) { #Only display $project of interest types.
 684                 $html .= _jstree_li_html($schema, $project_type_of_interest, $children{$child}->{'id'}, $children{$child}->{'name'})."</li>";
 685             }
 686         }
 687     }
 688     $html .= '</ul></li>';
 689     #print STDERR "Finished, returning with html at time ".localtime()."\n";
 690     return $html;
 691 }
 692
 693 sub _jstree_li_html {
 694     my $schema = shift;
 695     my $type = shift;
 696     my $id = shift;
 697     my $name = shift;
 698     # print STDERR "TYPE =".Dumper($type)."\n";
 699
 700     my $url = '#';
 701     if ($type eq 'trial' || $type eq 'genotyping_trial' || $type eq 'sampling_trial') {
 702         $url = "/breeders/trial/".$id;
 703     } elsif ($type eq 'folder') {
 704         $url = "/folder/".$id;
 705     } elsif ($type eq 'cross') {
 706         $url = "/cross/".$id;
 707     } elsif ($type eq 'analyses') {
 708         $url = "/analyses/".$id;
 709     } elsif ($type eq 'breeding_program') {
 710         $url = "/breeders/program/".$id;
 711     } elsif ($type eq 'genotyping_project') {
 712                 $url = "/breeders/trial/".$id;
 713     } elsif ($type eq 'activity' || $type eq 'transformation') {
 714         $url = "/breeders/trial/".$id;
 715     }
 716
 717     return "<li data-jstree='{\"type\":\"$type\"}' id=\"$id\"><a href=\"$url\">".$name.'</a>';
 718 }
 719
 720
 721
 722
 723 __PACKAGE__->meta->make_immutable();
 724
 725 1;