lib/CXGN/Stock/SequencingInfo.pm

   1
   2 =head1 NAME
   3
   4 CXGN::Stock::SequencingInfo - a class to match keys to a standardized JSON structure
   5
   6 =head1 DESCRIPTION
   7
   8 The stockprop of type "sequencing_project_info" is stored as JSON. This class maps keys to the JSON structure and retrieves and saves the stockprop.
   9
  10 =head1 EXAMPLE
  11
  12   my $si = CXGN::Stock::SequencingInfo->new( { schema => $schema, $stockprop_id });
  13
  14 =head1 AUTHOR
  15
  16  Lukas Mueller <lam87@cornell.edu>
  17
  18 =cut
  19
  20 package CXGN::Stock::SequencingInfo;
  21
  22 use Moose;
  23 use JSON::Any;
  24 use Data::Dumper;
  25 use SGN::Model::Cvterm;
  26
  27 =head1 ACCESSORS
  28
  29 =head2 schema
  30
  31 =head2 stock_id
  32
  33 =head2 stockprop_id
  34
  35 =head2 organization
  36
  37 =head2 website
  38
  39 =head2 genbank_accession
  40
  41 =head2 funded_by
  42
  43 =head2 funder_project_id
  44
  45 =head2 contact_email
  46
  47 =head2 sequencing_year
  48
  49 =head2 publication
  50
  51 =head2 jbrowse_link
  52
  53 =head2 blast_db_id
  54
  55 =cut
  56
  57 has 'schema' => (isa => 'Ref', is => 'rw', required => 1);
  58
  59 has 'stockprop_id' => (isa => 'Maybe[Int]', is => 'rw');
  60
  61 has 'stock_id' => (isa => 'Int', is => 'rw');
  62
  63 has 'type_id' => (isa => 'Int', is => 'rw');
  64
  65 has 'type' => (isa => 'Str', is => 'ro', default => "sequencing_project_info" );
  66
  67 has 'organization' => (isa => 'Maybe[Str]', is => 'rw');
  68
  69 has 'website' => (isa => 'Maybe[Str]', is => 'rw');
  70
  71 has 'genbank_accession' => (isa => 'Maybe[Str]', is => 'rw');
  72
  73 has 'funded_by' => (isa => 'Maybe[Str]', is => 'rw');
  74
  75 has 'funder_project_id' => (isa => 'Maybe[Str]', is => 'rw');
  76
  77 has 'contact_email' => (isa => 'Maybe[Str]', is => 'rw');
  78
  79 has 'sequencing_year' => (isa => 'Maybe[Str]', is => 'rw');
  80
  81 has 'publication' => (isa => 'Maybe[Str]', is => 'rw');
  82
  83 has 'jbrowse_link' => (isa => 'Maybe[Str]', is => 'rw');
  84
  85 has 'blast_db_id' => (isa => 'Maybe[Int]', is => 'rw');
  86
  87 has 'allowed_fields' => (isa => 'Ref', is => 'ro', default =>  sub {  [ qw | organization website genbank_accession funded_by funder_project_id contact_email sequencing_year publication jbrowse_link blast_db_id stockprop_id stock_id | ] } );
  88
  89
  90 sub BUILD {
  91     my $self = shift;
  92     my $args = shift;
  93
  94     if ($args->{stockprop_id} eq "undefined") { $args->{stockprop_id} = undef; }
  95
  96     print STDtERR "STOCKPROPID: ".$self->stockprop_id.", TYPE: ".$self->type()."\n";
  97     my $type_id = SGN::Model::Cvterm->get_cvterm_row($self->schema(), $self->type(), 'stock_property')->cvterm_id();
  98
  99     $self->type_id($type_id);
 100
 101     $self->_load_object();
 102
 103     $self->stockprop_id($args->{stockprop_id});
 104 }
 105
 106
 107 =head2 Class methods
 108
 109
 110 =head2 get_sequencing_project_infos($schema, $stock_id)
 111
 112  Usage:        my @seq_projects = $se_info->get_sequencing_project_infos($schema, $stock_id);
 113  Desc:
 114  Ret:
 115  Args:
 116  Side Effects:
 117  Example:
 118
 119 =cut
 120
 121 sub get_sequencing_project_infos {
 122     my $class = shift;
 123     my $schema = shift;
 124     my $stock_id = shift;
 125
 126     my @stockprops = $class->_retrieve_stockprops($schema, $stock_id, "sequencing_project_info");
 127
 128     print STDERR "Stockprops = ".Dumper(\@stockprops);
 129
 130     my @infos = ();
 131     foreach my $sp (@stockprops) {
 132         my $hash;
 133
 134         my $json = $sp->[1];
 135
 136         eval {
 137             $hash = JSON::Any->jsonToObj($json);
 138         };
 139         $hash->{stockprop_id} = $sp->[0];
 140         $hash->{uniquename} = $schema->resultset("Stock::Stock")->find( { stock_id => $stock_id })->uniquename();
 141         if ($@) {
 142             print STDERR "Warning: $json is not valid json in stockprop ".$sp->[0].".!\n";
 143         }
 144         push @infos, $hash;
 145     }
 146
 147     print STDERR "Hashes = ".Dumper(\@infos);
 148     return \@infos;
 149 }
 150
 151 =head2 all_sequenced_stocks()
 152
 153  Usage:        @sequenced_stocks = CXGN::Stock->sequenced_stocks();
 154  Desc:
 155  Ret:
 156  Args:
 157  Side Effects:
 158  Example:
 159
 160 =cut
 161
 162 sub all_sequenced_stocks {
 163     my $class = shift;
 164     my $schema = shift;
 165
 166     print STDERR "all_sequenced_stocks with ".ref($schema)." as parameter...\n";
 167     my $type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'sequencing_project_info', 'stock_property')->cvterm_id();
 168     print STDERR "type_id = $type_id\n";
 169
 170     my $sp_rs = $schema->resultset("Stock::Stockprop")->search({ type_id => $type_id });
 171
 172     my @sequenced_stocks = ();
 173     while (my $row = $sp_rs->next()) {
 174         print STDERR "found stock with stock_id ".$row->stock_id()."\n";
 175         push @sequenced_stocks, $row->stock_id();
 176     }
 177
 178     return @sequenced_stocks;
 179 }
 180
 181
 182 =head2 OBJECT METHODS
 183
 184 =head2 method store()
 185
 186  Usage:         $s->set_sequencing_project_info($si, $stockprop_id)
 187  Desc:          creates a sequencing project info in the stockprop
 188  Ret:
 189  Args:          a CXGN::Stock::SequencingInfo object, and an optional
 190                 stockprop_id (which will trigger an update instead
 191                 of insert)
 192  Side Effects:
 193  Example:
 194
 195 =cut
 196
 197 sub store {
 198     my $self = shift;
 199
 200     if (!$self->stock_id()) {
 201         die "Need a stock_id to save SequencingInfo object.";
 202     }
 203
 204     if ($self->stockprop_id()) {
 205         # update
 206         print STDERR "updating stockprop...\n";
 207         my $row = $self->schema()->resultset("Stock::Stockprop")->find( { stockprop_id => $self->stockprop_id() } );
 208         if ($row) {
 209             $row->value($self->to_json());
 210             $row->update();
 211         }
 212     }
 213     else {
 214         # insert
 215         print STDERR "inserting stockprop...\n";
 216         my $row = $self->schema()->resultset("Stock::Stockprop")->create(
 217             {
 218                 stock_id => $self->stock_id(),
 219                 type_id => $self->type_id(),
 220                 value => $self->to_json()
 221             });
 222
 223         $self->stockprop_id($row->stockprop_id());
 224         $self->stock_id($row->stock_id());
 225         return $row->stockprop_id();
 226     }
 227
 228 }
 229
 230 =head2 method delete()
 231
 232  Usage:
 233  Desc:
 234  Ret:
 235  Args:
 236  Side Effects:
 237  Example:
 238
 239 =cut
 240
 241 sub delete {
 242     my $self = shift;
 243
 244     print STDERR "CXGN::Stock::SequencingInfo: Deleting sequencing info object ".$self->stockprop_id()."\n";
 245     my $stockprop;
 246
 247     print STDERR "stock_id = ".$self->stock_id().", stockprop_id = ".$self->stockprop_id()."\n";
 248
 249     eval {
 250         $stockprop = $self->schema()->resultset("Stock::Stockprop")->find({ type_id=>$self->type_id(), stock_id => $self->stock_id(), stockprop_id=>$self->stockprop_id() });
 251
 252     };
 253     if ($@) {
 254         die "Delete failed!\n";
 255     }
 256
 257     if (!$stockprop) {
 258         print STDERR "No such stockprop associated with such type or stock. Not deleting.\n";
 259         return 0;
 260     }
 261     else {
 262         print STDERR "Deleting stcokprop now.\n";
 263         $stockprop->delete();
 264         print STDERR "SequencingInfo successfully deleted.\n";
 265         return 1;
 266     }
 267 }
 268
 269 =head2 _load_object
 270
 271  Desc:
 272  Ret:
 273  Args:
 274  Side Effects:   requires stockprop_id and schema to be set
 275  Example:
 276
 277 =cut
 278
 279 sub _load_object {
 280     my $self= shift;
 281
 282     print STDERR "_load_object...\n";
 283
 284     print STDERR "Stockprop_id is now ".$self->stockprop_id()."\n";
 285     if ($self->stockprop_id()) {
 286         print STDERR "configuring object...\n";
 287         my $stockprop_type_id = SGN::Model::Cvterm->get_cvterm_row($self->schema, $self->type(), 'stock_property')->cvterm_id();
 288         my $rs = $self->schema->resultset("Stock::Stockprop")->search({ stockprop_id => $self->stockprop_id(), type_id => $stockprop_type_id } );
 289
 290         if ($rs->count() == 0) { die "No stockprops could be retrieved." }
 291
 292         my $row = $rs->next(); # should only be one
 293
 294         $self->type_id($stockprop_type_id);
 295         $self->stock_id($row->stock_id());
 296         $self->from_json($row->value());
 297     }
 298 }
 299
 300
 301
 302
 303 =head2 _retrieve_stockprops
 304
 305  Usage:
 306  Desc:         Retrieves stockprop as a list of [stockprop_id, value]
 307  Ret:
 308  Args:
 309  Side Effects:
 310  Example:
 311
 312 =cut
 313
 314 sub _retrieve_stockprops {
 315     my $class = shift;
 316     my $schema = shift;
 317     my $stock_id = shift;
 318     my $type = shift;
 319
 320     my @results;
 321
 322     print STDERR "_retrieve_stockprops...\n";
 323
 324     eval {
 325         my $stockprop_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, $type, 'stock_property')->cvterm_id();
 326         my $rs = $schema->resultset("Stock::Stockprop")->search({ stock_id => $stock_id, type_id => $stockprop_type_id }, { order_by => {-asc => 'stockprop_id'} });
 327
 328         while (my $r = $rs->next()){
 329             push @results, [ $r->stockprop_id(), $r->value() ];
 330         }
 331     };
 332
 333     if ($@)  {
 334         print STDERR "Cvterm $type does not exist in this database\n";
 335     };
 336
 337     return @results;
 338 }
 339
 340 =head2 from_json
 341
 342  Usage:
 343  Desc:
 344  Ret:
 345  Args:
 346  Side Effects:
 347  Example:
 348
 349 =cut
 350
 351 sub from_json {
 352     my $self = shift;
 353     my $json = shift;
 354
 355     my $data = JSON::Any->decode($json);
 356
 357     $self->from_hash($data);
 358 }
 359
 360 =head2 from_hash
 361
 362  Usage:
 363  Desc:
 364  Ret:
 365  Args:
 366  Side Effects:
 367  Example:
 368
 369 =cut
 370
 371 sub from_hash {
 372     my $self = shift;
 373     my $hash = shift;
 374
 375     my $allowed_fields = $self->allowed_fields();
 376
 377     print STDERR Dumper($hash);
 378
 379     foreach my $f (@$allowed_fields) {
 380         print STDERR "Processing $f ($hash->{$f})...\n";
 381         if ($hash->{$f} eq "undefined") { $hash->{$f} = undef; }
 382         $self->$f($hash->{$f});
 383     }
 384 }
 385
 386 =head2 to_json
 387
 388  Usage:
 389  Desc:
 390  Ret:
 391  Args:
 392  Side Effects:
 393  Example:
 394
 395 =cut
 396
 397 sub to_json {
 398     my $self = shift;
 399
 400     my $allowed_fields = $self->allowed_fields();
 401
 402     print STDERR Dumper($allowed_fields);
 403     my $data;
 404
 405     foreach my $f (@$allowed_fields) {
 406         if (defined($self->$f())) {
 407             $data->{$f} = $self->$f();
 408         }
 409     }
 410
 411     my $json = JSON::Any->encode($data);
 412     return $json;
 413 }
 414
 415 =head2 to_hash
 416
 417  Usage:
 418  Desc:
 419  Ret:
 420  Args:
 421  Side Effects:
 422  Example:
 423
 424 =cut
 425
 426 sub to_hashref {
 427     my $self = shift;
 428
 429     my $hashref;
 430     foreach my $f (@{$self->allowed_fields()}) {
 431         $hashref->{$f} = $self->$f;
 432     }
 433     return $hashref;
 434 }
 435
 436 =head2 validate
 437
 438  Usage:
 439  Desc:
 440  Ret:
 441  Args:
 442  Side Effects:
 443  Example:
 444
 445 =cut
 446
 447 sub validate {
 448     my $self = shift;
 449
 450     my @errors = ();
 451     my @warnings = ();
 452
 453     # check keys in the info hash...
 454     if (!defined($self->sequencing_year())) {
 455         push @errors, "Need year for sequencing project";
 456     }
 457     if (!defined($self->organization())) {
 458         push @errors, "Need organization for sequencing project";
 459     }
 460     if (!defined($self->website())) {
 461         push @errors, "Need website for sequencing project";
 462     }
 463     if (!defined($self->publication())) {
 464         push @warnings, "Need publication for sequencing project";
 465     }
 466     if (!defined($self->website())) {
 467         push @warnings, "Need project url for sequencing project";
 468     }
 469     if (!defined($self->jbrowse_link())) {
 470         push @warnings, "Need jbrowse link for sequencing project";
 471     }
 472
 473     if (@errors) {
 474         die join("\n", @errors);
 475     }
 476 }
 477
 478
 479
 480 1;
 481
 482
 483