Registry.pm 45.8 KB
Newer Older
Ian Longden's avatar
Ian Longden committed
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
#
# Ensembl module for Registry
#
# Copyright EMBL/EBI
##
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

=head1 NAME

Bio::EnsEMBL::Registry

=head1 SYNOPSIS

16 17
Bio::EnsEMBL::Registry->load_all("configuration_file");

18 19
$gene_adaptor =
  Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "gene" );
Ian Longden's avatar
Ian Longden committed
20 21 22 23


=head1 DESCRIPTION

24 25
All Adaptors are stored/registered using this module. This module should
then be used to get the adaptors needed.
Ian Longden's avatar
Ian Longden committed
26

27 28
The registry can be loaded from a configuration file using the load_all
method.
Ian Longden's avatar
Ian Longden committed
29

30 31 32 33
If a filename is passed to load_all then this is used.  Else if the
enviroment variable ENSEMBL_REGISTRY is set to the name on an existing
configuration file, then this is used.  Else if the file .ensembl_init
in your home directory exist, it is used.
Ian Longden's avatar
Ian Longden committed
34

35 36
For the Web server ENSEMBL_REGISTRY should be set in SiteDefs.pm.  This
will then be passed on to load_all.
37 38


39 40 41 42 43
The registry can also be loaded via the method load_registry_from_db
which given a database host will load the latest versions of the Ensembl
databases from it.

The four types of registries are for db adaptors, dba adaptors, dna adaptors
Ian Longden's avatar
Ian Longden committed
44 45 46 47
and the standard type.

=head2 db

48
These are registries for backwards compatibility and enable the subroutines
49
to add other adaptors to connections. 
Ian Longden's avatar
Ian Longden committed
50 51 52 53 54

e.g. get_all_db_adaptors, get_db_adaptor, add_db_adaptor, remove_db_adaptor
are the old DBAdaptor subroutines which are now redirected to the Registry.

So if before we had
55 56

    my $sfa = $self->adaptor()->db()->get_db_adaptor('blast');
Ian Longden's avatar
Ian Longden committed
57 58

We now want to change this to
59 60 61

    my $sfa =
      Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "blast" );
Ian Longden's avatar
Ian Longden committed
62 63 64 65 66 67 68 69 70


=head2 DBA

These are the stores for the DBAdaptors

The Registry will create all the DBConnections needed now if you set up the
configuration correctly. So instead of the old commands like

71 72
    my $db           = Bio::EnsEMBL::DBSQL::DBAdaptor->new(...);
    my $exon_adaptor = $db->get_ExonAdaptor;
Ian Longden's avatar
Ian Longden committed
73 74 75

we should now have just

76 77
    my $exon_adaptor =
      Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "exon" );
Ian Longden's avatar
Ian Longden committed
78 79 80 81 82


=head2 DNA

This is an internal Registry and allows the configuration of a dnadb. 
Steve Trevanion's avatar
Steve Trevanion committed
83
An example here is to set the est database to get its dna data from the core database.
Ian Longden's avatar
Ian Longden committed
84

85 86 87
    ## set the est db to use the core for getting dna data.
    # Bio::EnsEMBL::Utils::ConfigRegistry->dnadb_add(
    #         "Homo Sapiens", "core", "Homo Sapiens", "est" );
Ian Longden's avatar
Ian Longden committed
88 89 90 91 92 93 94 95 96


=head2 adaptors

This is the registry for all the general types of adaptors like GeneAdaptor, ExonAdaptor, 
Slice Adaptor etc.

These are accessed by the get_adaptor subroutine i.e.

97 98
    my $exon_adaptor =
      Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "exon" );
Ian Longden's avatar
Ian Longden committed
99 100 101 102 103 104 105 106 107 108 109 110 111 112 113

=head1 CONTACT

Post questions to the Ensembl developer list: <ensembl-dev@ebi.ac.uk>


=head1 METHODS

=cut


package Bio::EnsEMBL::Registry;

use strict;

114
use Bio::EnsEMBL::DBSQL::DBAdaptor;
Ian Longden's avatar
Ian Longden committed
115 116
use Bio::EnsEMBL::Utils::Exception qw( deprecate throw warning );
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
117
use Bio::EnsEMBL::Utils::ConfigRegistry;
118
use DBI;
Ian Longden's avatar
Ian Longden committed
119

120 121
use Config::IniFiles;

Ian Longden's avatar
Ian Longden committed
122 123
use vars qw(%registry_register);

Glenn Proctor's avatar
Glenn Proctor committed
124
my $API_VERSION = 45;
125

Ian Longden's avatar
Ian Longden committed
126 127

=head2 load_all
128

129 130 131 132 133 134 135 136
 Will load the registry with the configuration file which is obtained
 from the first in the following and in that order.

  1) If an argument is passed to this method, this is used as the name
     of the configuration file to read.

  2) If the enviroment variable ENSEMBL_REGISTRY is set, this is used as
     the name of the configuration file to read.
Ian Longden's avatar
Ian Longden committed
137

138 139
  3) If the file .ensembl_init exist in the home directory, it is used
     as the configuration file.
Ian Longden's avatar
Ian Longden committed
140

141 142 143 144 145 146 147 148
  Arg [1]    : (optional) string
               Name of file to load the registry from.
  Arg [2]    : (optional) integer
               If not 0, will print out all information.
  Arg [3]    : (optional) integer
               If not 0, the db connection will not be cleared, if 0 or
               if not set the db connections will be cleared (this is
               the default).
Ian Longden's avatar
Ian Longden committed
149 150 151
  Example    : Bio::EnsEMBL::Registry->load_all();
  Returntype : none
  Exceptions : none
152
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
153 154

=cut
155

156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194
sub load_all {
    my $class = shift;
    my ( $config_file, $verbose, $no_clear ) = @_;

    $config_file ||= $ENV{ENSEMBL_REGISTRY}
      || $ENV{HOME} . "/.ensembl_init";

    $verbose  ||= 0;
    $no_clear ||= 0;

    if ( !defined($config_file) ) {
        if ($verbose) {
            print( STDERR
                   "No default registry configuration to load.\n" );
        }
    } elsif ( !-e $config_file ) {
        if ($verbose) {
            printf( STDERR "Configuration file '%s' does not exist. "
                      . "Registry configuration not loaded.\n",
                    $config_file );
        }
    } else {
        if ( defined( $registry_register{'seen'} ) ) {
            if ( !$no_clear ) {
                if ($verbose) {
                    print( STDERR "Clearing previously loaded "
                           . "registry configuration\n" );
                }
                $class->clear();
            }
        }
        $registry_register{'seen'} = 1;

        if ($verbose) {
            printf( STDERR
                      "Loading registry configuration from '%s'.\n",
                    $config_file );
        }

195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222
        my $cfg = Config::IniFiles->new( -file => $config_file );
        if ( defined $cfg ) {

            # This is a map from group names to Ensembl DB adaptors.
            my %group2adaptor = (
                 'blast'   => 'Bio::EnsEMBL::External::BlastAdaptor',
                 'compara' => 'Bio::EnsEMBL::Compara::DBSQL::DBAdaptor',
                 'core'    => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
                 'estgene' => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
                 'funcgen' => 'Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor',
                 'haplotype' =>
                   'Bio::EnsEMBL::ExternalData::Haplotype::DBAdaptor',
                 'hive' => 'Bio::EnsEMBL::Hive::DBSQL::DBAdaptor',
                 'lite' => 'Bio::EnsEMBL::Lite::DBAdaptor',
                 'otherfeatures' => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
                 'pipeline' =>
                   'Bio::EnsEMBL::Pipeline::DBSQL::DBAdaptor',
                 'snp' =>
                   'Bio::EnsEMBL::ExternalData::SNPSQL::DBAdaptor',
                 'variation' =>
                   'Bio::EnsEMBL::Variation::DBSQL::DBAdaptor',
                 'vega' => 'Bio::EnsEMBL::DBSQL::DBAdaptor' );

            my %default_adaptor_args = ();

            if ( $cfg->SectionExists('default') ) {
                # The 'default' section is special.  It contain default
                # values that should be implicit to all other section in
223 224 225 226 227 228 229 230 231 232 233 234 235
                # this configuration file.  Aliases are added if there
                # is also a 'species' setting.

                my $alias = $cfg->val( 'default', 'alias' );
                $cfg->delval( 'default', 'alias' );

                my $species = $cfg->val( 'default', 'species' );

                if ( defined($alias) && defined($species) ) {
                    Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
                                     -species => $species,
                                     -alias => [ split( /\n/, $alias ) ]
                    );
236
                }
237

238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268
                %default_adaptor_args =
                  map { '-' . $_ => $cfg->val( 'default', $_ ) }
                  $cfg->Parameters('default');
            }

            foreach my $section ( $cfg->Sections() ) {
                if ( $section eq 'default' )
                {    # We have already done the 'default' section.
                    next;
                }

                my $group = $cfg->val( $section, 'group' )
                  || $cfg->val( 'default', 'group' );

                if ( !defined($group) ) {
                    printf( STDERR "Key 'group' is undefined "
                              . "for configuration section '%s', "
                              . "skipping this section.\n",
                            $section );
                    next;
                }

                my $adaptor = $group2adaptor{ lc($group) };
                if ( !defined($adaptor) ) {
                    printf( STDERR "Unknown group '%s' "
                              . "for configuration section '%s', "
                              . "skipping this section.\n",
                            $group, $section );
                    next;
                }

269 270 271 272 273
                # Handle aliases.  A section must have both an 'alias'
                # setting and a 'species' setting for aliases to be
                # added.  The 'species' setting might be inherited from
                # the 'default' section.

274 275 276
                my $alias = $cfg->val( $section, 'alias' );
                $cfg->delval( $section, 'alias' );

277 278 279 280 281 282 283 284 285 286 287
                my $species = $cfg->val( $section, 'species' )
                  || $cfg->val( 'default', 'species' );

                if ( defined($alias) && defined($species) ) {
                    Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
                                     -species => $species,
                                     -alias => [ split( /\n/, $alias ) ]
                    );
                }

                # Fill in the adaptor initialization arguments.
288 289 290 291 292 293 294 295 296 297 298 299 300
                # We trust the user to provide sensible key-value pairs.
                my %adaptor_args = %default_adaptor_args;
                foreach my $parameter ( $cfg->Parameters($section) ) {
                    $adaptor_args{ '-' . $parameter } =
                      $cfg->val( $section, $parameter );
                }

                if ($verbose) {
                    printf( "Configuring adaptor '%s' "
                              . "for configuration section '%s'...\n",
                            $adaptor, $section );
                }

301
                require($adaptor);
302 303 304 305 306 307 308 309 310 311 312 313 314 315 316
                $adaptor->new(%adaptor_args);

            } ## end foreach my $section ( $cfg->Sections...
        } else {
            # This is probably no ini-file but an old style piece
            # of configuration written in Perl.  We need to try to
            # require() it.

            eval { require($config_file) };
            if ($@) { die($@) }

            # To make the web code avoid doing this again:
            delete $INC{$config_file};
        }
    } ## end else [ if ( !defined($config_file...
317
} ## end sub load_all
318 319

=head2 clear
320

321 322 323 324 325
 Will clear the registry and disconnect from all databases.

  Example    : Bio::EnsEMBL::Registry->clear();
  Returntype : none
  Exceptions : none
326
  Status     : Stable
327 328 329 330 331 332 333 334 335 336 337

=cut

sub clear{
  my ($self);
  
  foreach my $dba (@{$registry_register{'_DBA'}}){
    if($dba->dbc->connected){
      $dba->dbc->db_handle->disconnect();
    }
  }
Ian Longden's avatar
Ian Longden committed
338
  %registry_register = ();
Ian Longden's avatar
Ian Longden committed
339 340 341
}

#
342
# db adaptors. (for backwards compatibility)
Ian Longden's avatar
Ian Longden committed
343 344 345 346
#

=head2 add_db

347
  Arg [1]    : db (DBAdaptor) to add adaptor to.
Ian Longden's avatar
Ian Longden committed
348 349 350 351 352
  Arg [2]    : name of the name to add the adaptor to in the registry.
  Arg [3]    : The adaptor to be added to the registry.
  Example    : Bio::EnsEMBL::Registry->add_db($db, "lite", $dba);
  Returntype : none
  Exceptions : none
353
  Status     : At Risk.
354
             : This is here for backwards compatibility only and may be removed 
355 356 357
             : eventually. Solution is to make sure the db and the adaptor have
             : the same species and the call is then no longer needed.
             
Ian Longden's avatar
Ian Longden committed
358 359 360 361 362 363
=cut

sub add_db{
  my ($class, $db, $name, $adap) = @_;


364 365
  if(lc($db->species()) ne lc($adap->species)){
    $registry_register{lc($db->species())}{lc($db->group())}{'_special'}{lc($name)} = $adap;
366
  }
Ian Longden's avatar
Ian Longden committed
367 368 369 370
}

=head2 remove_db

371
  Arg [1]    : db (DBAdaptor) to remove adaptor from.
Ian Longden's avatar
Ian Longden committed
372 373 374 375
  Arg [2]    : name to remove the adaptor from in the registry.
  Example    : my $db = Bio::EnsEMBL::Registry->remove_db($db, "lite");
  Returntype : adaptor
  Exceptions : none
376
  Status     : At Risk.
377
             : This is here for backwards compatibility only and may be removed 
378 379
             : eventually. Solution is to make sure the db and the adaptor have
             : the same species and the call is then no longer needed.
Ian Longden's avatar
Ian Longden committed
380 381 382 383 384 385

=cut

sub remove_db{
  my ($class, $db, $name) = @_;

386 387
  my $ret = $registry_register{lc($db->species())}{lc($db->group())}{'_special'}{lc($name)};
  $registry_register{lc($db->species())}{lc($db->group())}{'_special'}{lc($name)} = undef;
Ian Longden's avatar
Ian Longden committed
388 389 390 391 392 393

  return $ret;
}

=head2 get_db

394
  Arg [1]    : db (DBAdaptor) to get adaptor from.
Ian Longden's avatar
Ian Longden committed
395 396 397 398
  Arg [2]    : name to get the adaptor for in the registry.
  Example    : my $db = Bio::EnsEMBL::Registry->get_db("Human", "core", "lite");
  Returntype : adaptor
  Exceptions : none
399
  Status     : At Risk.
400
             : This is here for backwards compatibility only and may be removed 
401 402
             : eventually. Solution is to make sure the db and the adaptor have
             : the same species then call get_DBAdaptor instead.
Ian Longden's avatar
Ian Longden committed
403 404 405 406 407 408

=cut

sub get_db{
  my ($class, $db, $name) = @_;

409
  my $ret = Bio::EnsEMBL::Registry->get_DBAdaptor(lc($db->species),lc($name));
410 411 412 413

  if(defined($ret)){
    return $ret;
  }
414
  return $registry_register{lc($db->species())}{lc($db->group())}{'_special'}{lc($name)};
Ian Longden's avatar
Ian Longden committed
415 416 417 418
}

=head2 get_all_db_adaptors

419
  Arg [1]    : db (DBAdaptor) to get all the adaptors from.
Ian Longden's avatar
Ian Longden committed
420 421 422
  Example    : my $db = Bio::EnsEMBL::Registry->get_all_db_adaptors($db);
  Returntype : adaptor
  Exceptions : none
423
  Status     : At Risk.
424
             : This is here for backwards compatibility only and may be removed 
425 426 427
             : eventually. Solution is to make sure the dbs all have
             : the same species then call get_all_DBAdaptors(-species => "human");

Ian Longden's avatar
Ian Longden committed
428 429 430 431 432 433 434

=cut

sub get_all_db_adaptors{
  my ($class,$db) = @_;
  my %ret=();

Ian Longden's avatar
Ian Longden committed
435 436 437 438
# we now also want to add all the DBAdaptors for the same species.
# as add_db_adaptor does not add if it is from the same species.

  foreach my $dba (@{$registry_register{'_DBA'}}){
439
    if(lc($dba->species()) eq lc($db->species())){
Ian Longden's avatar
Ian Longden committed
440 441 442 443
      $ret{$dba->group()} = $dba;
    } 
  }

444
 foreach my $key (keys %{$registry_register{$class->get_alias($db->species())}{lc($db->group())}{'_special'}}){
445
   $ret{$key} = $registry_register{$class->get_alias($db->species())}{lc($db->group())}{'_special'}{$key};
Ian Longden's avatar
Ian Longden committed
446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463
 }

  return \%ret;
}


#
# DBAdaptors
#

=head2 add_DBAdaptor

  Arg [1]    : name of the species to add the adaptor to in the registry.
  Arg [2]    : name of the group to add the adaptor to in the registry.
  Arg [3]    : The DBAaptor to be added to the registry.
  Example    : Bio::EnsEMBL::Registry->add_DBAdaptor("Human", "core", $dba);
  Returntype : none
  Exceptions : none
464 465
  caller     : internal
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
466 467 468 469 470 471

=cut

sub add_DBAdaptor{
  my ($class, $species, $group, $adap) = @_;

472 473 474 475 476
  if(!($class->alias_exists($species))){
    $class->add_alias($species,$species);
  }
  

Ian Longden's avatar
Ian Longden committed
477 478
  $species = $class->get_alias($species);

479
  $registry_register{$species}{lc($group)}{'_DB'} = $adap;
Ian Longden's avatar
Ian Longden committed
480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500

  if(!defined($registry_register{'_DBA'})){
    my @list =();
    push(@list,$adap);
    $registry_register{'_DBA'}= \@list;
  }
  else{
    push(@{$registry_register{'_DBA'}},$adap);
  }

}



=head2 get_DBAdaptor

  Arg [1]    : name of the species to get the adaptor for in the registry.
  Arg [2]    : name of the group to get the adaptor for in the registry.
  Example    : $dba = Bio::EnsEMBL::Registry->get_DBAdaptor("Human", "core");
  Returntype : DBAdaptor
  Exceptions : none
501
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
502 503 504 505 506 507 508 509

=cut

sub get_DBAdaptor{
  my ($class, $species, $group) = @_;

  $species = $class->get_alias($species);

510 511
  return  $registry_register{$species}{lc($group)}{'_DB'};

Ian Longden's avatar
Ian Longden committed
512 513 514 515
}

=head2 get_all_DBAdaptors

516 517 518 519 520 521 522 523
  Arg [SPECIES]: (optional) string 
                  species name to get adaptors for
  Arg [GROUP]  : (optional) string 
                  group name to get adaptors for
  Example      : @dba = @{Bio::EnsEMBL::Registry->get_all_DBAdaptors()};
               : @human_dbas = @{Bio::EnsEMBL::Registry->get_all_DBAdaptors(-species => 'human')};
  Returntype   : list of DBAdaptors
  Exceptions   : none
524
  Status       : Stable
Ian Longden's avatar
Ian Longden committed
525 526 527 528

=cut

sub get_all_DBAdaptors{
529 530
  my ($class,@args)=@_;
  my @ret;
Ian Longden's avatar
Ian Longden committed
531

532 533 534 535 536 537
  my ($species, $group) = 
    rearrange([qw(SPECIES GROUP)], @args);
  if(defined($species)){
    $species = $class->get_alias($species);
  }
  foreach my $dba (@{$registry_register{'_DBA'}}){
538
    if(!defined($species) || lc($species) eq lc($dba->species)){
539 540 541 542 543 544 545 546
      if(!defined($group) || lc($group) eq lc($dba->group)){
	push @ret, $dba;
      }
    }
  }


  return \@ret;
Ian Longden's avatar
Ian Longden committed
547 548
}

549 550 551 552 553 554
=head2 get_all_DBAdaptors_by_connection

  Arg [1]    :dbconnection to use to find DBAdaptors
  Returntype : reference to list of DBAdaptors
  Exceptions : none.
  Example    : @dba = @{Bio::EnsEMBL::Registry->get_all_DBAdaptors_by_connection($dbc);
555
  Status     : Stable
556 557 558 559 560 561 562 563 564

=cut

sub get_all_DBAdaptors_by_connection{
  my ($self, $dbc_orig) = @_;
  my @return;

  foreach my $dba ( @{$registry_register{'_DBA'}}){
    my $dbc = $dba->dbc;
Web Admin's avatar
Web Admin committed
565
    if($dbc && $dbc->can('equals') && $dbc->equals($dbc_orig)){
566 567 568 569 570 571 572
      push @return, $dba;
    }
  }
  return \@return;
}


Ian Longden's avatar
Ian Longden committed
573 574 575 576 577 578 579 580
#
# DNA Adaptors
#

=head2 add_DNAAdaptor

  Arg [1]    : name of the species to add the adaptor to in the registry.
  Arg [2]    : name of the group to add the adaptor to in the registry.
581 582 583
  Arg [3]    : name of the species to get the dna from
  Arg [4]    : name of the group to get the dna from
  Example    : Bio::EnsEMBL::Registry->add_DNAAdaptor("Human", "estgene", "Human", "core");
Ian Longden's avatar
Ian Longden committed
584 585
  Returntype : none
  Exceptions : none
586
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
587 588 589 590

=cut

sub add_DNAAdaptor{
Ian Longden's avatar
Ian Longden committed
591
  my ($class, $species, $group, $dnadb_species, $dnadb_group) = @_;
Ian Longden's avatar
Ian Longden committed
592 593

  $species = $class->get_alias($species);
594
  $dnadb_species = $class->get_alias($dnadb_species);
595
  if($dnadb_group->isa('Bio::EnsEMBL::DBSQL::DBAdaptor')){
Ian Longden's avatar
Ian Longden committed
596
    deprecated("");
597 598
  }
  else{
599 600
    $registry_register{$species}{lc($group)}{'_DNA'} = $dnadb_group;
    $registry_register{$species}{lc($group)}{'_DNA2'} = $dnadb_species;
601
  }
Ian Longden's avatar
Ian Longden committed
602 603 604 605 606 607 608 609 610
}

=head2 get_DNAAdaptor

  Arg [1]    : name of the species to get the adaptor for in the registry.
  Arg [2]    : name of the group to get the adaptor for in the registry.
  Example    : $dnaAdap = Bio::EnsEMBL::Registry->get_DNAAdaptor("Human", "core");
  Returntype : adaptor
  Exceptions : none
611
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
612 613 614 615 616 617 618

=cut

sub get_DNAAdaptor{
  my ($class, $species, $group) = @_;

  $species = $class->get_alias($species);
619 620
  my $new_group = $registry_register{$species}{lc($group)}{'_DNA'};
  my $new_species = $registry_register{$species}{lc($group)}{'_DNA2'};
621
  if( defined $new_group ) {
Ian Longden's avatar
Ian Longden committed
622
    return  $class->get_DBAdaptor($new_species,$new_group);
623 624 625
  } else {
    return undef;
  }
Ian Longden's avatar
Ian Longden committed
626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641
}

#
# General Adaptors
#

=head2 add_adaptor

  Arg [1]    : name of the species to add the adaptor to in the registry.
  Arg [2]    : name of the group to add the adaptor to in the registry.
  Arg [3]    : name of the type to add the adaptor to in the registry.
  Arg [4]    : The DBAaptor to be added to the registry.
  Arg [5]    : (optional) if set okay to overwrite.
  Example    : Bio::EnsEMBL::Registry->add_adaptor("Human", "core", "Gene", $adap);
  Returntype : none
  Exceptions : none
642 643
  Caller     : internal
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660


=cut

sub add_adaptor{
  my ($class,$species,$group,$type,$adap, $reset)= @_;

  $species = $class->get_alias($species);

#
# Becouse the adaptors are not stored initially only there class paths when
# the adaptors are obtained we need to store these instead.
# It is not necessarily an error if the registry is overwritten without
# the reset set but it is an indication that we are overwriting a database
# which should be a warning for now
#

661
  if(defined($reset)){ # JUST REST THE HASH VALUE NO MORE PROCESSING NEEDED
662
    $registry_register{$species}{lc($group)}{lc($type)} = $adap;
Ian Longden's avatar
Ian Longden committed
663 664
    return;
  }
665
  if(defined($registry_register{$species}{lc($group)}{lc($type)})){ 
Glenn Proctor's avatar
Glenn Proctor committed
666
    #print STDERR ("Overwriting Adaptor in Registry for $species $group $type\n");
667
    $registry_register{$species}{lc($group)}{lc($type)} = $adap;
Ian Longden's avatar
Ian Longden committed
668 669
   return;
  }
670
  $registry_register{$species}{lc($group)}{lc($type)} = $adap;
Ian Longden's avatar
Ian Longden committed
671 672 673

  if(!defined ($registry_register{$species}{'list'})){
    my @list =();
674
    push(@list,$type);
Ian Longden's avatar
Ian Longden committed
675 676 677
    $registry_register{$species}{'list'}= \@list;
  }
  else{
678
    push(@{$registry_register{$species}{'list'}},$type);
Ian Longden's avatar
Ian Longden committed
679 680
  }

681

Ian Longden's avatar
Ian Longden committed
682

683
  if(!defined ($registry_register{lc($type)}{$species})){
Ian Longden's avatar
Ian Longden committed
684 685
    my @list =();
    push(@list,$adap);
686
    $registry_register{lc($type)}{$species}= \@list;
Ian Longden's avatar
Ian Longden committed
687 688
  }
  else{
689
    push(@{$registry_register{lc($type)}{$species}},$adap);
Ian Longden's avatar
Ian Longden committed
690 691 692 693 694 695 696 697 698 699 700 701 702
  }

}


=head2 get_adaptor

  Arg [1]    : name of the species to add the adaptor to in the registry.
  Arg [2]    : name of the group to add the adaptor to in the registry.
  Arg [3]    : name of the type to add the adaptor to in the registry.
  Example    : $adap = Bio::EnsEMBL::Registry->get_adaptor("Human", "core", "Gene");
  Returntype : adaptor
  Exceptions : none
703
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
704 705 706 707 708 709

=cut

sub get_adaptor{
  my ($class,$species,$group,$type)= @_;
 
710
  $species = $class->get_alias($species);
711
  my %dnadb_adaptors = qw(sequence  1 assemblymapper 1  karyotypeband 1 repeatfeature 1 coordsystem 1  assemblyexceptionfeature 1 );
712

713
  my $dnadb_group =  $registry_register{$species}{lc($group)}{_DNA};
714

715 716
  if( defined($dnadb_group) && defined($dnadb_adaptors{lc($type)}) ) {
      $species = $registry_register{$species}{lc($group)}{'_DNA2'};
717
      $group = $dnadb_group;
Ian Longden's avatar
Ian Longden committed
718 719
  }

720
  my $ret = $registry_register{$species}{lc($group)}{lc($type)};
Ian Longden's avatar
Ian Longden committed
721
  if(!defined($ret)){
722
    return undef;
Ian Longden's avatar
Ian Longden committed
723 724
  }
  if(!ref($ret)){ # not instantiated yet
725
    my $dba = $registry_register{$species}{lc($group)}{'_DB'};
Ian Longden's avatar
Ian Longden committed
726 727 728 729 730 731 732
    my $module = $ret;
    eval "require $module";

    if($@) {
      warning("$module cannot be found.\nException $@\n");
      return undef;
    }
733 734 735 736
    if(!defined($registry_register{$species}{lc($group)}{'CHECKED'})){
      $registry_register{$species}{lc($group)}{'CHECKED'} = 1;
      $class->version_check($dba);
    }
Ian Longden's avatar
Ian Longden committed
737 738 739 740 741 742 743 744 745 746
    my $adap = "$module"->new($dba);
    Bio::EnsEMBL::Registry->add_adaptor($species, $group, $type, $adap, "reset");
    $ret = $adap;
  }

  return $ret;
}

=head2 get_all_adaptors

747 748 749 750 751 752
  Arg [SPECIES] : (optional) string 
                  species name to get adaptors for
  Arg [GROUP] : (optional) string 
                  group name to get adaptors for
  Arg [TYPE] : (optional) string 
                  type to get adaptors for
Ian Longden's avatar
Ian Longden committed
753
  Example    : @adaps = @{Bio::EnsEMBL::Registry->get_all_adaptors()};
754
  Returntype : ref to list of adaptors
Ian Longden's avatar
Ian Longden committed
755
  Exceptions : none
756
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
757 758 759 760

=cut

sub get_all_adaptors{
761 762 763 764
  my ($class,@args)= @_;
  my ($species, $group, $type);
  my @ret=();
  my (%species_hash, %group_hash, %type_hash);
Ian Longden's avatar
Ian Longden committed
765

766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798

  if(@args == 1){ #old species only one parameter
    warn("-SPECIES argument should now be used to get species adaptors");
    $species = $args[0];
  }
  else{
    # new style -SPECIES, -GROUP, -TYPE
    ($species, $group, $type) =
      rearrange([qw(SPECIES GROUP TYPE)], @args);
  }

  if(defined($species)){
    $species_hash{$species} = 1;
  }
  else{
    # get list of species
    foreach my $dba (@{$registry_register{'_DBA'}}){
      $species_hash{lc($dba->species())} = 1;
    }
  }
  if(defined($group)){
    $group_hash{$group} = 1;
  }
  else{
    foreach my $dba (@{$registry_register{'_DBA'}}){
      $group_hash{lc($dba->group())} = 1;
    }
  }
  if(defined($type)){
    $type_hash{$type} =1;
  }
  else{
    foreach my $dba (@{$registry_register{'_DBA'}}){ 
799
	foreach my $ty (@{$registry_register{lc($dba->species)}{'list'}}){
800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816
	  $type_hash{lc($ty)} = 1;
	}
      }
  }
  
  ### NOW NEED TO INSTANTIATE BY CALLING get_adaptor
  foreach my $sp (keys %species_hash){
    foreach my $gr (keys %group_hash){
      foreach my $ty (keys %type_hash){
	my $temp = $class->get_adaptor($sp,$gr,$ty);
	if(defined($temp)){
	  push @ret, $temp;
	}
      }
    }
  }
  return (\@ret);
Ian Longden's avatar
Ian Longden committed
817 818 819 820 821 822 823 824 825 826 827
}


=head2 add_alias

  Arg [1]    : name of the species to add alias for
  Arg [2]    : name of the alias
  Example    : Bio::EnsEMBL::Registry->add_alias("Homo Sapiens","Human");
  Description: add alternative name for the species.
  Returntype : none
  Exceptions : none
828
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
829 830 831 832 833 834

=cut

sub add_alias{
  my ($class, $species,$key) = @_;

835
  $registry_register{'_ALIAS'}{lc($key)} = lc($species);
Ian Longden's avatar
Ian Longden committed
836 837 838 839 840 841 842 843
}

=head2 get_alias

  Arg [1]    : name of the possible alias to get species for
  Example    : Bio::EnsEMBL::Registry->get_alias("Human");
  Description: get proper species name.
  Returntype : species name
844
  Exceptions : none
845
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
846 847 848 849

=cut

sub get_alias{
850
  my ($class, $key) = @_;
Ian Longden's avatar
Ian Longden committed
851

852
  if(!defined($registry_register{'_ALIAS'}{lc($key)})){
853
    return $key;
Ian Longden's avatar
Ian Longden committed
854
  }
855
  return $registry_register{'_ALIAS'}{lc($key)};
Ian Longden's avatar
Ian Longden committed
856
}
857 858 859 860

=head2 alias_exists

  Arg [1]    : name of the possible alias to get species for
Ian Longden's avatar
Ian Longden committed
861
  Example    : Bio::EnsEMBL::Registry->alias_exists("Human");
862 863 864
  Description: does the species name exist.
  Returntype : 1 if exists else 0
  Exceptions : none
865
  Status     : Stable
866 867 868 869 870 871

=cut

sub alias_exists{
  my ($class, $key) = @_;

872
  if(defined($registry_register{'_ALIAS'}{lc($key)})){
873 874 875 876
    return 1;
  }
  return 0;
}
877

878 879 880 881 882 883 884
=head2 set_disconnect_when_inactive

  Example    : Bio::EnsEMBL::Registry->set_disconnect_when_inactive();
  Description: Set the flag to make sure that the database connection is dropped if
               not being used on each database.
  Returntype : none
  Exceptions : none
885
  Status     : Stable
886 887 888

=cut

889
sub set_disconnect_when_inactive{
890
  foreach my $dba ( @{get_all_DBAdaptors()}){
891 892
    my $dbc = $dba->dbc;
    #disconnect if connected
893
    $dbc->disconnect_if_idle() if $dbc->connected();
894 895 896
    $dbc->disconnect_when_inactive(1);
  }
}
Ian Longden's avatar
Ian Longden committed
897

898 899 900 901 902 903 904

=head2 disconnect_all

  Example    : Bio::EnsEMBL::Registry->disconnect_all();
  Description: disconnect from all the databases.
  Returntype : none
  Exceptions : none
905
  Status     : Stable
906 907 908

=cut

909
sub disconnect_all {
Web Admin's avatar
fixed  
Web Admin committed
910
  foreach my $dba ( @{get_all_DBAdaptors()||[]} ){
911
    my $dbc = $dba->dbc;
Web Admin's avatar
Web Admin committed
912
    next unless $dbc;
913 914 915 916
    #disconnect if connected
    $dbc->disconnect_if_idle() if $dbc->connected();
  }
}
917

918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935
=head2 change_access

  Will change the username and password for a set of databases.
  if host,user or database names are missing then these are not checked.
  So for example if you do not specify a database then ALL databases on
  the specified  host and port will be changed.

  Arg [1]    : name of the host to change access on
  Arg [2]    : port number to change access on
  Arg [3]    : name of the user to change access on
  Arg [4]    : name of the database to change access on
  Arg [5]    : name of the new user
  Arg [6]    : new password

  Example    : Bio::EnsEMBL::Registry->get_alias("Human");
  Description: change username and password on one or more databases
  Returntype : none
  Exceptions : none
936
  Status     : Stable
937 938 939 940

=cut

sub change_access{
Steve Trevanion's avatar
Steve Trevanion committed
941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956
my $self = shift;
    my ($host,$port,$user,$dbname,$new_user,$new_pass) = @_;
    foreach my $dba ( @{$registry_register{'_DBA'}}){
	my $dbc = $dba->dbc;
	if((!defined($host) or $host eq $dbc->host) and
	   (!defined($port) or $port eq $dbc->port) and
	   (!defined($user) or $user eq $dbc->username) and
	   (!defined($dbname) or $dbname eq $dbc->dbname)){
	    if($dbc->connected()){
		$dbc->db_handle->disconnect();
		$dbc->connected(undef);
	    }
	    # over write the username and password
	    $dbc->username($new_user);
	    $dbc->password($new_pass);
	}
957 958 959
    }
}

960 961


962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000 1001 1002 1003 1004 1005
=head2 load_registry_from_url

  Arg [1]    : string $url
  Example : load_registry_from_url("mysql://anonymous@ensembldb.ensembl.org:3306");
  Description: Will load the correct versions of the ensembl databases for the
               software release it can find on a database instance into the 
               registry. Also adds a set of standard aliases. The url format is:
               mysql://[[username][:password]@]hostname[:port].
               You can also request a specific version for the databases by adding
               a slash and the version number but your script may crash as the API
               version won't match the DB version.
  Exceptions : None.
  Status     : Stable
 
=cut

sub load_registry_from_url {
  my ($self, $url, $verbose) = @_;

  if ($url =~ /mysql\:\/\/([^\@]+\@)?([^\:\/]+)(\:\d+)?(\/\d+)?/) {
    my $user_pass = $1;
    my $host = $2;
    my $port = $3;
    my $version = $4;

    $user_pass =~ s/\@$//;
    my ($user, $pass) = $user_pass =~ m/([^\:]+)(\:.+)?/;
    $pass =~ s/^\:// if ($pass);
    $port =~ s/^\:// if ($port);
    $version =~ s/^\/// if ($version);

    $self->load_registry_from_db(
        -host=> $host,
        -user => $user,
        -pass => $pass,
        -port => $port,
        -db_version => $version,
        -verbose => $verbose);
  } else {
    throw("Only MySQL URLs are accepted at the moment");
  }
}


1006
=head2 load_registry_from_db
1007

1008 1009 1010 1011 1012 1013 1014 1015 1016
  Arg [HOST] : The domain name of the database host to connect to.
               
  Arg [USER] : string
               The name of the database user to connect with
  Arg [PASS] : (optional) string
               The password to be used to connect to the database
  Arg [PORT] : int
               The port to use when connecting to the database
  Arg [VERBOSE]: (optional) Wether to print database messages 
1017 1018 1019 1020 1021 1022
  Arg [DB_VERSION]: (optional) By default, only databases corresponding
               to this API version are loaded. This allows the script to
               use databases from another version although it might not
               work properly. This option should only be used for
               production or testing purposes and if you really know what
               you are doing.
1023 1024 1025 1026 1027

  Example : load_registry_from_db( -host => 'ensembldb.ensembl.org',
				   -user => 'anonymous',
				   -verbose => "1" );

1028
  Description: Will load the correct versions of the ensembl databases for the
1029
               software release it can find on a database instance into the 
1030
               registry. Also adds a set of standard aliases.
1031 1032

  Exceptions : None.
1033
  Status     : Stable
1034 1035
 
=cut
1036

1037
sub load_registry_from_db {
1038
  my($self, @args) = @_;
1039 1040
  my ($host, $port, $user, $pass, $verbose, $db_version) =
    rearrange([qw(HOST PORT USER PASS VERBOSE DB_VERSION)], @args);
1041 1042 1043 1044 1045 1046 1047



  my $go_version = 0;
  my $compara_version =0;

  $user ||= "ensro";
1048
  $port ||= 3306;
1049 1050 1051 1052 1053 1054
  my $db = DBI->connect( "DBI:mysql:host=$host;port=$port" , $user, $pass );

  my $res = $db->selectall_arrayref( "show databases" );
  my @dbnames = map {$_->[0] } @$res;
  
  my %temp;
1055
  my $software_version = $self->software_version();
1056 1057 1058
  if (defined($db_version)) {
    $software_version = $db_version;
  }
1059
  print "Will only load $software_version databases\n" if ($verbose);
1060 1061
  for my $db (@dbnames){
    if($db =~ /^([a-z]+_[a-z]+_[a-z]+)_(\d+)_(\d+[a-z]*)/){
1062
      if($2 eq $software_version){
1063 1064 1065 1066
	$temp{$1} = $2."_".$3;
      }
    }
    elsif($db =~ /^ensembl_compara_(\d+)/){
1067
      if($1 eq $software_version){
1068 1069 1070 1071
	$compara_version = $1;
      }
    }
    elsif($db =~ /^ensembl_go_(\d+)/){
1072
      if($1 eq $software_version){
1073 1074 1075 1076 1077 1078 1079 1080 1081 1082 1083 1084 1085 1086 1087 1088 1089 1090 1091 1092 1093 1094 1095 1096 1097 1098 1099 1100 1101
	$go_version = $1;
      }
    }
  }
  
  @dbnames =();
  
  foreach my $key ( keys %temp){
    push @dbnames, $key."_".$temp{$key};
  }	 
  # register core databases
  
  my @core_dbs = grep { /^[a-z]+_[a-z]+_core_\d+_/ } @dbnames;
  
  for my $coredb ( @core_dbs ) {
    my ($species, $num ) = ( $coredb =~ /(^[a-z]+_[a-z]+)_core_(\d+)/ );
    my $dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new
      ( -group => "core",
	-species => $species,
	-host => $host,
	-user => $user,
	-pass => $pass,
	-port => $port,
	-dbname => $coredb
      );
    (my $sp = $species ) =~ s/_/ /g;
    $self->add_alias( $species, $sp );
    print $coredb." loaded\n" if ($verbose);
  }
1102

1103 1104 1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 1116 1117 1118 1119 1120 1121 1122
  # register cdna databases
  
  my @cdna_dbs = grep { /^[a-z]+_[a-z]+_cdna_\d+_/ } @dbnames;
  
  for my $cdnadb ( @cdna_dbs ) {
    my ($species, $num ) = ( $cdnadb =~ /(^[a-z]+_[a-z]+)_cdna_(\d+)/ );
    my $dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new
      ( -group => "cdna",
	-species => $species,
	-host => $host,
	-user => $user,
	-pass => $pass,
	-port => $port,
	-dbname => $cdnadb
      );
    (my $sp = $species ) =~ s/_/ /g;
    $self->add_alias( $species, $sp );
    print $cdnadb." loaded\n" if ($verbose);
  }

1123 1124 1125 1126 1127 1128 1129 1130 1131 1132 1133 1134 1135 1136 1137 1138 1139
  my @vega_dbs = grep { /^[a-z]+_[a-z]+_vega_\d+_/ } @dbnames;
  
  for my $vegadb ( @vega_dbs ) {
    my ($species, $num ) = ( $vegadb =~ /(^[a-z]+_[a-z]+)_vega_(\d+)/ );
    my $dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new
      ( -group => "vega",
	-species => $species,
	-host => $host,
	-user => $user,
	-pass => $pass,
	-port => $port,
	-dbname => $vegadb
      );
    (my $sp = $species ) =~ s/_/ /g;
    $self->add_alias( $species, $sp );
    print $vegadb." loaded\n" if ($verbose);
  }
1140
  
Ian Longden's avatar
Ian Longden committed
1141
  my @other_dbs = grep { /^[a-z]+_[a-z]+_otherfeatures_\d+_/ } @dbnames;
1142
  
Ian Longden's avatar
Ian Longden committed
1143 1144
  for my $other_db ( @other_dbs ) {
    my ($species, $num) = ( $other_db =~ /(^[a-z]+_[a-z]+)_otherfeatures_(\d+)/ );
1145
    my $dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new
Ian Longden's avatar
Ian Longden committed
1146
      ( -group => "otherfeatures",
1147 1148 1149 1150 1151
	-species => $species,
	-host => $host,
	-user => $user,
	-pass => $pass,
	-port => $port,
Ian Longden's avatar
Ian Longden committed
1152
	-dbname => $other_db
1153
      );
1154 1155
      (my $sp = $species ) =~ s/_/ /g;
      $self->add_alias( $species, $sp );
1156
      print $other_db." loaded\n" if ($verbose);       
1157 1158 1159 1160 1161 1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181
  }
  
  
  eval "require Bio::EnsEMBL::Variation::DBSQL::DBAdaptor";
  if($@) {
    #ignore variations as code required not there for this
    print "Bio::EnsEMBL::Variation::DBSQL::DBAdaptor module not found so variation databases will be ignored if found\n" if ($verbose);
  }
  else{
    my @variation_dbs = grep { /^[a-z]+_[a-z]+_variation_\d+_/ } @dbnames;
    
    for my $variation_db ( @variation_dbs ) {
      my ($species, $num ) = ( $variation_db =~ /(^[a-z]+_[a-z]+)_variation_(\d+)/ );
      my $dba<