lib/CXGN/Trial/Folder.pm

   1
   2 package CXGN::Trial::Folder;
   3
   4 use CXGN::Chado::Cvterm;
   5
   6 use Moose;
   7 use SGN::Model::Cvterm;
   8 use Data::Dumper;
   9
  10 has 'bcs_schema' => ( isa => 'Bio::Chado::Schema',
  11         is => 'rw',
  12         required => 1,
  13 );
  14
  15 has 'folder_id' => (isa => "Int",
  16         is => 'rw',
  17 );
  18
  19 has 'children' => (is => 'rw',
  20         lazy => 1,
  21         default => sub {
  22                 my $self = shift;
  23                 $self->_get_children();
  24         }
  25 );
  26
  27 has 'is_folder' => (isa => 'Bool',
  28         is => 'rw',
  29         default => 0,
  30 );
  31
  32 has 'folder_type' => (isa => 'Str',
  33         is => 'rw',
  34 );
  35
  36 has 'name' => (isa => 'Str',
  37         is => 'rw',
  38         default => 'Untitled',
  39 );
  40
  41 has 'breeding_program_trial_relationship_id' =>  (isa => 'Int',
  42         is => 'rw',
  43 );
  44
  45 has 'project_parent' => (isa => 'Bio::Chado::Schema::Result::Project::Project',
  46         is => 'rw',
  47 );
  48
  49 has 'breeding_program' => (isa => 'Bio::Chado::Schema::Result::Project::Project',
  50         is => 'rw',
  51 );
  52
  53 has 'breeding_program_cvterm_id' => (isa => 'Int',
  54         is => 'rw',
  55 );
  56
  57 has 'folder_cvterm_id' => (isa => 'Int',
  58         is => 'rw',
  59 );
  60
  61
  62 sub BUILD {
  63         my $self = shift;
  64
  65         my $row = $self->bcs_schema()->resultset('Project::Project')->find( { project_id=>$self->folder_id() });
  66
  67         if (!$row) {
  68                 die "The specified folder with id ".$self->folder_id()." does not exist!";
  69         }
  70
  71         $self->name($row->name());
  72
  73         my $breeding_program_type_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema,'breeding_program', 'project_property')->cvterm_id();
  74         $self->breeding_program_cvterm_id($breeding_program_type_id);
  75
  76         my $folder_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema,'trial_folder', 'project_property')->cvterm_id();
  77         $self->folder_cvterm_id($folder_cvterm_id);
  78
  79         my $breeding_program_trial_relationship_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema,'breeding_program_trial_relationship', 'project_relationship')->cvterm_id();
  80         $self->breeding_program_trial_relationship_id($breeding_program_trial_relationship_id);
  81
  82         my $folder_type = $self->bcs_schema()->resultset('Project::Projectprop')-> search( { project_id => $self->folder_id() });
  83
  84         while (my $folder_type_row = $folder_type->next) {
  85                 if ($folder_type_row->type_id() == $self->folder_cvterm_id() ) {
  86                         $self->folder_type("folder");
  87                         $self->is_folder(1);
  88                 }
  89                 elsif ($folder_type_row->type_id() == $self->breeding_program_cvterm_id()) {
  90                         #print STDERR "Setting folder type to breeding_program.\n";
  91                         $self->folder_type("breeding_program");
  92                 }
  93         }
  94
  95         if (!$self->folder_type) {
  96                 my $cross_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema, 'cross',  'stock_type')->cvterm_id;
  97
  98                 my $trial_type_rs = $self->bcs_schema->resultset("Project::Project")->search({ 'me.project_id' => $self->folder_id })->search_related('projectprops');
  99                 while (my $tt = $trial_type_rs->next()) {
 100                         if ($tt->type_id == $cross_cvterm_id) {
 101                                 $self->folder_type("cross");
 102                         } elsif ($tt->value eq 'genotyping_plate') {
 103                                 $self->folder_type("genotyping_trial");
 104                         }
 105                 }
 106
 107                 if (!$self->folder_type) {
 108                         $self->folder_type("trial");
 109                 }
 110         }
 111
 112         my $breeding_program_rel_row = $self->bcs_schema()->resultset('Project::ProjectRelationship')->find( { subject_project_id => $self->folder_id(), type_id =>  $self->breeding_program_trial_relationship_id() });
 113         if ($breeding_program_rel_row) {
 114                 my $parent_row = $self->bcs_schema()->resultset('Project::Project')->find( { project_id=> $breeding_program_rel_row->object_project_id() });
 115                 $self->project_parent($parent_row);
 116                 $self->breeding_program($parent_row);
 117         }
 118
 119         my $folder_rel_row = $self->bcs_schema()->resultset('Project::ProjectRelationship')->find( { subject_project_id => $self->folder_id(), type_id =>  $self->folder_cvterm_id() });
 120         if ($folder_rel_row) {
 121                 my $parent_row = $self->bcs_schema()->resultset('Project::Project')->find( { project_id=> $folder_rel_row->object_project_id() });
 122                 $self->project_parent($parent_row);
 123         }
 124
 125 }
 126
 127 # class methods
 128
 129 sub create {
 130     my $class = shift;
 131     my $args = shift;
 132
 133     # check if name is already taken
 134     #
 135     my $check_rs = $args->{bcs_schema}->resultset('Project::Project')->search( { name => $args->{name} } );
 136
 137     if ($check_rs->count() > 0) {
 138         die "The name ".$args->{name}." cannot be used for a folder because it already exists.";
 139     }
 140
 141      my $folder_cvterm = SGN::Model::Cvterm->get_cvterm_row($args->{bcs_schema},'trial_folder', 'project_property');
 142
 143     my $project_row = $args->{bcs_schema}->resultset('Project::Project')->create(
 144         {
 145             name =>  $args->{name},
 146             description => $args->{description} || "",
 147         });
 148
 149     my $project_id = $project_row->project_id();
 150
 151     my $folder_projectprop_row = $args->{bcs_schema}->resultset('Project::Projectprop')->create(
 152         {
 153             project_id => $project_id,
 154             type_id => $folder_cvterm->cvterm_id() }
 155         );
 156
 157     my $folder = CXGN::Trial::Folder->new( { bcs_schema => $args->{bcs_schema}, folder_id => $project_id });
 158
 159     $folder->associate_parent($args->{parent_folder_id});
 160     $folder->associate_breeding_program($args->{breeding_program_id});
 161
 162     return $folder;
 163 }
 164
 165
 166 sub list {
 167     my $class = shift;
 168     my $args = shift;
 169                 my $schema = $args->{bcs_schema};
 170
 171     my $folder_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema,'trial_folder', 'project_property')->cvterm_id();
 172                 my $breeding_program_trial_relationship_id = SGN::Model::Cvterm->get_cvterm_row($schema,'breeding_program_trial_relationship', 'project_relationship')->cvterm_id();
 173
 174                 my $breeding_program_rel;
 175                 if ($args->{breeding_program_id}) {
 176                         $breeding_program_rel = $schema->resultset('Project::ProjectRelationship')->search({ 'me.object_project_id' => $args->{breeding_program_id}, 'me.type_id' => $breeding_program_trial_relationship_id })->search_related("subject_project")->search_related("projectprops", {'projectprops.type_id'=>$folder_cvterm_id}, {'+select'=>'subject_project.name', '+as'=>'name' } );
 177                 } else {
 178                         $breeding_program_rel = $schema->resultset('Project::ProjectRelationship')->search({ 'me.type_id' => $breeding_program_trial_relationship_id })->search_related("subject_project")->search_related("projectprops", {'projectprops.type_id'=>$folder_cvterm_id}, {'+select'=>'subject_project.name', '+as'=>'name' } );
 179                 }
 180
 181
 182     my @folders;
 183     while (my $row = $breeding_program_rel->next()) {
 184                         push @folders, [ $row->project_id(), $row->get_column('name') ];
 185     }
 186
 187     return @folders;
 188 }
 189
 190
 191
 192 ### OBJECT METHODS
 193
 194
 195 # return a resultset with children of the folder
 196 #
 197 sub _get_children {
 198         my $self = shift;
 199
 200         my @children;
 201
 202         my $rs = $self->bcs_schema()->resultset("Project::Project")->search_related( 'project_relationship_subject_projects', { object_project_id => $self->folder_id() }, { order_by => 'me.name' });
 203
 204         @children = map { $_->subject_project_id() } $rs->all();
 205
 206         my @child_folders;
 207         foreach my $id (@children) {
 208                 my $folder = CXGN::Trial::Folder->new( { bcs_schema=> $self->bcs_schema(), folder_id=>$id });
 209
 210                 if ($self->folder_type() eq "breeding_program") {
 211                         if ($folder->project_parent()) {
 212                                 if ($folder->project_parent()->name() eq $self->name()) {
 213                                         #print STDERR "Pushing ".$folder->name().$folder->folder_type."\n";
 214                                         push @child_folders, $folder;
 215                                 }
 216                         }
 217                 } else {
 218                         #print STDERR "parent is not a breeding program... pushing ".$folder->name().$folder->folder_type."...\n";
 219                         push @child_folders, $folder;
 220                 }
 221         }
 222
 223         return \@child_folders;
 224 }
 225
 226 sub associate_parent {
 227     my $self = shift;
 228                 my $parent_id = shift;
 229
 230                 my $folder_cvterm_id = $self->folder_cvterm_id();
 231                 my $breeding_program_trial_relationship_id = $self->breeding_program_trial_relationship_id();
 232
 233                 #If the user selects 'None' to remove the trial from the folder, then the parent_id will be passed as 0. No new parent will be created.
 234                 if ($parent_id == 0) {
 235                         $self->remove_parents;
 236                         return;
 237                 }
 238
 239                 my $parent_row = $self->bcs_schema()->resultset("Project::Project")->find( { project_id => $parent_id } );
 240
 241                 if (!$parent_row) {
 242                         print STDERR "The folder specified as parent does not exist";
 243                         return;
 244                 }
 245
 246                 my $parentprop_row = $self->bcs_schema()->resultset("Project::Projectprop")->find( { project_id => $parent_id,  type_id => { -in => [ $folder_cvterm_id, $breeding_program_trial_relationship_id ] } } );
 247
 248                 if (!$parentprop_row) {
 249                         print STDERR "The specified parent folder is not of type folder or breeding program. Ignoring.";
 250                         return;
 251                 }
 252
 253                 $self->remove_parents;
 254
 255                 my $project_rel_row = $self->bcs_schema()->resultset('Project::ProjectRelationship')->create({
 256             object_project_id => $parent_id,
 257             subject_project_id => $self->folder_id(),
 258             type_id => $folder_cvterm_id,
 259                 });
 260                 $project_rel_row->insert();
 261
 262     $self->project_parent($parent_row);
 263
 264                 my $parent_is_child = check_if_folder_is_child_in_tree($self->bcs_schema, $parent_id, $self->children());
 265                 if ($parent_is_child) {
 266                         print STDERR 'Parent '.$parent_id.' is child in tree of folder '.$self->folder_id()."\n";
 267                         my $parent_folder = CXGN::Trial::Folder->new({
 268                                 bcs_schema => $self->bcs_schema,
 269                                 folder_id => $parent_id
 270                         });
 271                         $parent_folder->remove_parents;
 272                 }
 273
 274 }
 275
 276 sub remove_parents {
 277         my $self = shift;
 278         #Remove any previous parents
 279         my $project_rels = $self->bcs_schema()->resultset('Project::ProjectRelationship')->search({
 280                 subject_project_id => $self->folder_id(),
 281                 type_id => $self->folder_cvterm_id()
 282         });
 283
 284         if ($project_rels->count() > 0) {
 285                 while (my $p = $project_rels->next()) {
 286                         print STDERR $p->subject_project_id." : ".$p->object_project_id." : Removing parent folder association...\n";
 287                         $p->delete();
 288                 }
 289         }
 290         return;
 291 }
 292
 293 sub check_if_folder_is_child_in_tree {
 294         my $schema = shift;
 295         my $folder_id = shift;
 296         my $children = shift;
 297         foreach (@$children) {
 298                 my $child_folder_id = $_->folder_id();
 299                 if ($child_folder_id == $folder_id) {
 300                         return 1;
 301                 } else{
 302                         #print STDERR $child_folder_id."\n";
 303                         my $child_folder = CXGN::Trial::Folder->new({
 304                                 bcs_schema => $schema,
 305                                 folder_id => $child_folder_id
 306                         });
 307                         return check_if_folder_is_child_in_tree($schema, $folder_id, $child_folder->children() );
 308                 }
 309         }
 310
 311         return;
 312 }
 313
 314 sub associate_breeding_program {
 315     my $self = shift;
 316     my $breeding_program_id = shift;
 317
 318     if (!$breeding_program_id) {
 319         print STDERR "No breeding_program_id provided. Ignoring association.\n";
 320         return;
 321     }
 322
 323     my $project_rel_row = $self->bcs_schema()->resultset('Project::ProjectRelationship')->find(
 324         { object_project_id => $breeding_program_id,
 325           subject_project_id =>  $self->folder_id(),
 326         });
 327
 328     if (! $project_rel_row) {
 329         #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";
 330         $project_rel_row = $self->bcs_schema()->resultset('Project::ProjectRelationship')->create(
 331             {
 332                 object_project_id => $breeding_program_id,
 333                 subject_project_id => $self->folder_id(),
 334                 type_id => $self->breeding_program_trial_relationship_id(),
 335             });
 336
 337         $project_rel_row->insert();
 338     }
 339     else {
 340         $project_rel_row->object_project_id($breeding_program_id);
 341         $project_rel_row->update();
 342     }
 343
 344     my $row = $self->bcs_schema()->resultset('Project::Project')->find( { project_id=> $project_rel_row->object_project_id() });
 345     $self->breeding_program($row);
 346
 347 }
 348
 349 sub delete_folder {
 350         my $self = shift;
 351
 352         my $children = $self->children();
 353         if (scalar(@$children) > 0) {
 354                 return;
 355         }
 356         my $delete_folder = $self->bcs_schema->resultset("Project::Project")->find({ project_id => $self->folder_id })->delete();
 357         return 1;
 358 }
 359
 360 sub remove_parent {
 361
 362
 363 }
 364
 365
 366 sub remove_child {
 367
 368
 369 }
 370
 371 sub get_jstree_html {
 372         my $self = shift;
 373         my $parent_type = shift;
 374         my $project_type_of_interest = shift // 'trial';
 375
 376         my $html = "";
 377
 378         $html .= $self->_jstree_li_html($parent_type, $self->folder_id(), $self->name());
 379         $html .= "<ul>";
 380         my $children = $self->children();
 381
 382         if (@$children > 0) {
 383                 foreach my $child (@$children) {
 384                         if ($child->is_folder()) {
 385                                 $html .= $child->get_jstree_html('folder', $project_type_of_interest);
 386                         }
 387                         else {
 388                                 #Only display $project of interest types.
 389                                 if ($child->folder_type eq $project_type_of_interest) {
 390                                         $html .= $self->_jstree_li_html($child->folder_type(), $child->folder_id(), $child->name())."</li>";
 391                                 }
 392                         }
 393                 }
 394         }
 395         $html .= '</ul></li>';
 396         return $html;
 397 }
 398
 399 sub _jstree_li_html {
 400     my $self = shift;
 401     my $type = shift;
 402     my $id = shift;
 403     my $name = shift;
 404
 405     my $url = '#';
 406     if ($type eq 'trial') {
 407         $url = "/breeders/trial/".$id;
 408     } elsif ($type eq 'folder') {
 409         $url = "/folder/".$id;
 410     } elsif ($type eq 'cross') {
 411                 print STDERR "$id : $name \n";
 412                 my $cross_type_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema(), 'cross', 'stock_type')->cvterm_id();
 413                 my $cross_stock = $self->bcs_schema->resultset("Project::Project")->search({ 'me.project_id' => $id })->search_related('nd_experiment_projects')->search_related('nd_experiment')->search_related('nd_experiment_stocks')->search_related('stock', {'stock.type_id'=>$cross_type_id})->first();
 414                 if ($cross_stock) {
 415                         $id = $cross_stock->stock_id();
 416                 $url = "/cross/".$id;
 417                         return "<li data-jstree='{\"type\":\"$type\"}' id=\"$id\"><a href=\"$url\">".$name.'</a>';
 418                 } else {
 419                         return;
 420                 }
 421     }
 422
 423     return "<li data-jstree='{\"type\":\"$type\"}' id=\"$id\"><a href=\"$url\">".$name.'</a>';
 424 }
 425
 426
 427
 428
 429 __PACKAGE__->meta->make_immutable();
 430
 431 1;