Registry.pm 76.5 KB
Newer Older
1
=head1 LICENSE
Ian Longden's avatar
Ian Longden committed
2

3
  Copyright (c) 1999-2010 The European Bioinformatics Institute and
4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

    http://www.ensembl.org/info/about/code_licence.html

=head1 CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <ensembl-dev@ebi.ac.uk>.

  Questions may also be sent to the Ensembl help desk at
  <helpdesk@ensembl.org>.

=cut
Ian Longden's avatar
Ian Longden committed
20 21 22 23 24 25 26

=head1 NAME

Bio::EnsEMBL::Registry

=head1 SYNOPSIS

27
  use Bio::EnsEMBL::Registry;
28

29 30 31 32 33
  my $registry = 'Bio::EnsEMBL::Registry';

  $registry->load_all("configuration_file");

  $gene_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Gene' );
Ian Longden's avatar
Ian Longden committed
34 35 36

=head1 DESCRIPTION

37 38
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
39

40 41
The registry can be loaded from a configuration file using the load_all
method.
Ian Longden's avatar
Ian Longden committed
42

43 44 45 46
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
47

48 49
For the Web server ENSEMBL_REGISTRY should be set in SiteDefs.pm.  This
will then be passed on to load_all.
50 51


52 53 54 55
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.

56 57
The four types of registries are for db adaptors, dba adaptors, dna
adaptors and the standard type.
Ian Longden's avatar
Ian Longden committed
58 59 60

=head2 db

61 62
These are registries for backwards compatibility and enable the
subroutines to add other adaptors to connections.
Ian Longden's avatar
Ian Longden committed
63

64 65 66
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.
Ian Longden's avatar
Ian Longden committed
67 68

So if before we had
69

70
  my $sfa = $self->adaptor()->db()->get_db_adaptor('blast');
Ian Longden's avatar
Ian Longden committed
71 72

We now want to change this to
73

74 75
  my $sfa =
    Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "blast" );
Ian Longden's avatar
Ian Longden committed
76 77 78 79 80 81


=head2 DBA

These are the stores for the DBAdaptors

82 83
The Registry will create all the DBConnections needed now if you set up
the configuration correctly. So instead of the old commands like
Ian Longden's avatar
Ian Longden committed
84

85 86
  my $db           = Bio::EnsEMBL::DBSQL::DBAdaptor->new(...);
  my $exon_adaptor = $db->get_ExonAdaptor;
Ian Longden's avatar
Ian Longden committed
87 88 89

we should now have just

90 91
  my $exon_adaptor =
    Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "exon" );
Ian Longden's avatar
Ian Longden committed
92 93 94 95


=head2 DNA

96 97 98
This is an internal Registry and allows the configuration of a dnadb.
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
99

100 101 102
  ## 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
103 104 105 106


=head2 adaptors

107 108
This is the registry for all the general types of adaptors like
GeneAdaptor, ExonAdaptor, Slice Adaptor etc.
Ian Longden's avatar
Ian Longden committed
109 110 111

These are accessed by the get_adaptor subroutine i.e.

112 113
  my $exon_adaptor =
    Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "exon" );
Ian Longden's avatar
Ian Longden committed
114 115 116 117 118 119 120 121 122

=head1 METHODS

=cut

package Bio::EnsEMBL::Registry;

use strict;

123
use Bio::EnsEMBL::DBSQL::DBAdaptor;
Ian Longden's avatar
Ian Longden committed
124 125
use Bio::EnsEMBL::Utils::Exception qw( deprecate throw warning );
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
126
use Bio::EnsEMBL::Utils::ConfigRegistry;
127 128
use Bio::EnsEMBL::ApiVersion;

129
use DBI;
Ian Longden's avatar
Ian Longden committed
130 131 132

use vars qw(%registry_register);

133 134
# This is a map from group names to Ensembl DB adaptors.  Used by
# load_all() and reset_DBAdaptor().
135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150
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',
  'ontology'      => 'Bio::EnsEMBL::DBSQL::OntologyDBAdaptor',
  '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',
);
151 152


Ian Longden's avatar
Ian Longden committed
153
=head2 load_all
154

155 156
 Will load the registry with the configuration file which is
 obtained from the first in the following and in that order.
157

158 159
  1) If an argument is passed to this method, this is used as the
     name of the configuration file to read.
160

161 162
  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
163

164 165
  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
166

167 168
  Arg [1]    : (optional) string
               Name of file to load the registry from.
169

170 171
  Arg [2]    : (optional) integer
               If not 0, will print out all information.
172

173
  Arg [3]    : (optional) integer
174 175 176 177 178 179 180 181 182 183 184 185 186 187
               If not 0, the database connection will not be
               cleared, if 0 or if not set the database connections
               will be cleared (this is the default).

  Arg [4]:     (optional) boolean
               This option will turn off caching for slice features,
               so, every time a set of features is retrieved,
               they will come from the database instead of the
               cache.  This option is only recommended for advanced
               users, specially if you need to store and retrieve
               features.  It might reduce performance when querying
               the database if not used properly.  If in doubt, do
               not use it or ask in ensembl-dev.

Ian Longden's avatar
Ian Longden committed
188 189 190
  Example    : Bio::EnsEMBL::Registry->load_all();
  Returntype : none
  Exceptions : none
191
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
192 193

=cut
194

195 196
sub load_all {
    my $class = shift;
197
    my ( $config_file, $verbose, $no_clear, $no_cache ) = @_;
198 199 200 201 202 203

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

    $verbose  ||= 0;
    $no_clear ||= 0;
204
    $no_cache ||= 0;
205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234

    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 );
        }

235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250
        my $cfg;

        eval { require Config::IniFiles };
        if ($@) {
          # The user does not have the 'Config::IniFiles' module.
          if ($verbose) {
            print( STDERR "No Config::IniFiles module found, "
                   . "assuming this is not an ini-file\n" );
          }
          # If the configuration file *is* an ini-file, we can expect a
          # load of compilation errors from the next eval...
        } else {
          # The user has the 'Config::IniFiles' module installed.  See
          # if this is an ini-file or not...
          $cfg = Config::IniFiles->new( -file => $config_file );
        }
251

252
        if ( defined $cfg ) {
253
		  my %default_adaptor_args = ();
254 255 256 257

            if ( $cfg->SectionExists('default') ) {
                # The 'default' section is special.  It contain default
                # values that should be implicit to all other section in
258 259 260 261 262 263 264 265 266 267 268 269 270
                # 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 ) ]
                    );
271
                }
272

273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303
                %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;
                }

304 305 306 307 308
                # 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.

309 310 311
                my $alias = $cfg->val( $section, 'alias' );
                $cfg->delval( $section, 'alias' );

312 313 314 315 316 317 318 319 320 321 322
                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.
323 324 325
                # We trust the user to provide sensible key-value pairs.
                my %adaptor_args = %default_adaptor_args;
                foreach my $parameter ( $cfg->Parameters($section) ) {
326 327 328 329 330 331 332 333
                  $adaptor_args{ '-' . $parameter } =
                    $cfg->val( $section, $parameter );

                  # when set, do not use the feature cache in the
                  # different adaptors
                  if ($no_cache) {
                    $adaptor_args{'-no_cache'} = 1;
                  }
334 335 336 337 338 339 340 341
                }

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

342 343 344
                eval "require $adaptor";
                if ($@) { die($@) }

345 346 347 348 349 350 351 352 353 354 355 356 357 358 359
                $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...
360
} ## end sub load_all
361 362

=head2 clear
363

364 365 366 367 368
 Will clear the registry and disconnect from all databases.

  Example    : Bio::EnsEMBL::Registry->clear();
  Returntype : none
  Exceptions : none
369
  Status     : Stable
370 371 372 373 374 375 376 377 378 379 380

=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
381
  %registry_register = ();
Ian Longden's avatar
Ian Longden committed
382 383 384
}

#
385
# db adaptors. (for backwards compatibility)
Ian Longden's avatar
Ian Longden committed
386 387 388 389
#

=head2 add_db

390
  Arg [1]    : db (DBAdaptor) to add adaptor to.
Ian Longden's avatar
Ian Longden committed
391 392 393 394 395
  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
396
  Status     : At Risk.
397 398 399 400
             : This is here for backwards compatibility only and may
             : be removed 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
401

402
=cut
Ian Longden's avatar
Ian Longden committed
403

404 405
sub add_db {
  my ( $class, $db, $name, $adap ) = @_;
Ian Longden's avatar
Ian Longden committed
406

407
  if ( lc( $db->species() ) ne lc( $adap->species ) ) {
408 409
    $registry_register{_SPECIES}{ lc( $db->species() ) }
      { lc( $db->group() ) }{'_special'}{ lc($name) } = $adap;
410
  }
Ian Longden's avatar
Ian Longden committed
411 412 413 414
}

=head2 remove_db

415
  Arg [1]    : db (DBAdaptor) to remove adaptor from.
Ian Longden's avatar
Ian Longden committed
416 417 418 419
  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
420
  Status     : At Risk.
421 422 423 424
             : This is here for backwards compatibility only and may
             : be removed 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
425 426 427

=cut

428 429 430 431
sub remove_db {
  my ( $class, $db, $name ) = @_;

  my $ret =
432 433
    $registry_register{_SPECIES}{ lc( $db->species() ) }
    { lc( $db->group() ) }{'_special'}{ lc($name) };
Ian Longden's avatar
Ian Longden committed
434

435 436
  $registry_register{_SPECIES}{ lc( $db->species() ) }
    { lc( $db->group() ) }{'_special'}{ lc($name) } = undef;
Ian Longden's avatar
Ian Longden committed
437 438 439 440 441 442

  return $ret;
}

=head2 get_db

443
  Arg [1]    : db (DBAdaptor) to get adaptor from.
Ian Longden's avatar
Ian Longden committed
444 445 446 447
  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
448
  Status     : At Risk.
449 450 451 452
             : This is here for backwards compatibility only and may
             : be removed 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
453 454 455

=cut

456 457
sub get_db {
  my ( $class, $db, $name ) = @_;
Ian Longden's avatar
Ian Longden committed
458

459 460
  my $ret = Bio::EnsEMBL::Registry->get_DBAdaptor( lc( $db->species ),
    lc($name) );
461

462 463
  if ( defined($ret) ) { return $ret }

464
  return $registry_register{_SPECIES}{ lc( $db->species() ) }
465
    { lc( $db->group() ) }{'_special'}{ lc($name) };
Ian Longden's avatar
Ian Longden committed
466 467 468 469
}

=head2 get_all_db_adaptors

470
  Arg [1]    : db (DBAdaptor) to get all the adaptors from.
Ian Longden's avatar
Ian Longden committed
471 472 473
  Example    : my $db = Bio::EnsEMBL::Registry->get_all_db_adaptors($db);
  Returntype : adaptor
  Exceptions : none
474
  Status     : At Risk.
475 476 477 478
             : This is here for backwards compatibility only and
             : may be removed eventually.  Solution is to make
             : sure the dbs all have the same species then call
             : get_all_DBAdaptors(-species => "human");
479

Ian Longden's avatar
Ian Longden committed
480 481 482

=cut

483 484 485
sub get_all_db_adaptors {
  my ( $class, $db ) = @_;
  my %ret = ();
Ian Longden's avatar
Ian Longden committed
486

487 488
  # 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.
Ian Longden's avatar
Ian Longden committed
489

490 491 492 493
  foreach my $dba ( @{ $registry_register{'_DBA'} } ) {
    if ( lc( $dba->species() ) eq lc( $db->species() ) ) {
      $ret{ $dba->group() } = $dba;
    }
Ian Longden's avatar
Ian Longden committed
494 495
  }

496
  foreach my $key (
497
    keys %{
498 499 500
      $registry_register{_SPECIES}
        { $class->get_alias( $db->species() ) }{ lc( $db->group() ) }
        {'_special'} } )
501 502
  {
    $ret{$key} =
503 504 505
      $registry_register{_SPECIES}
      { $class->get_alias( $db->species() ) }{ lc( $db->group() ) }
      {'_special'}{$key};
506
  }
Ian Longden's avatar
Ian Longden committed
507 508

  return \%ret;
509
} ## end sub get_all_db_adaptors
Ian Longden's avatar
Ian Longden committed
510 511 512 513 514 515 516 517 518 519 520 521 522 523


#
# 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
524 525
  caller     : internal
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
526 527 528

=cut

529 530
sub add_DBAdaptor {
  my ( $class, $species, $group, $adap ) = @_;
Ian Longden's avatar
Ian Longden committed
531

532 533
  if ( !( $class->alias_exists($species) ) ) {
    $class->add_alias( $species, $species );
534 535
  }

Ian Longden's avatar
Ian Longden committed
536 537
  $species = $class->get_alias($species);

538
  $registry_register{_SPECIES}{$species}{ lc($group) }{'_DB'} = $adap;
Ian Longden's avatar
Ian Longden committed
539

540 541 542 543 544 545
  if ( !defined( $registry_register{'_DBA'} ) ) {
    my @list = ();
    push( @list, $adap );
    $registry_register{'_DBA'} = \@list;
  } else {
    push( @{ $registry_register{'_DBA'} }, $adap );
Ian Longden's avatar
Ian Longden committed
546 547 548 549 550 551 552 553 554 555 556 557 558
  }

}



=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
559
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
560 561 562

=cut

563 564
sub get_DBAdaptor {
  my ( $class, $species, $group ) = @_;
565
throw 'arrggh for '.$species if ! defined $species;
Ian Longden's avatar
Ian Longden committed
566 567
  $species = $class->get_alias($species);

568
  return $registry_register{_SPECIES}{$species}{ lc($group) }{'_DB'};
Ian Longden's avatar
Ian Longden committed
569 570 571 572
}

=head2 get_all_DBAdaptors

573 574 575 576
  Arg [SPECIES]: (optional) string 
                  species name to get adaptors for
  Arg [GROUP]  : (optional) string 
                  group name to get adaptors for
577 578 579 580 581 582 583 584 585
  Example      : 
                @dba =
                  @{ Bio::EnsEMBL::Registry->get_all_DBAdaptors() };

                @human_dbas =
                  @{ Bio::EnsEMBL::Registry->get_all_DBAdaptors(
                    -species => 'human'
                  ) };

586 587
  Returntype   : list of DBAdaptors
  Exceptions   : none
588
  Status       : Stable
Ian Longden's avatar
Ian Longden committed
589 590 591

=cut

592 593 594 595
sub get_all_DBAdaptors {
  my ( $class, @args ) = @_;

  my ( $species, $group ) = rearrange( [qw(SPECIES GROUP)], @args );
Ian Longden's avatar
Ian Longden committed
596

597
  if ( defined($species) ) { $species = $class->get_alias($species) }
598

599
  my @ret;
600
  foreach my $dba ( @{ $registry_register{'_DBA'} } ) {
601 602 603 604
    if ( ( !defined($species) || lc($species) eq lc( $dba->species() ) )
      && ( !defined($group) || lc($group) eq lc( $dba->group() ) ) )
    {
      push( @ret, $dba );
605 606 607 608
    }
  }

  return \@ret;
Ian Longden's avatar
Ian Longden committed
609 610
}

611 612
=head2 get_all_DBAdaptors_by_connection

613
  Arg [1]    : DBConnection used to find DBAdaptors
614
  Returntype : reference to list of DBAdaptors
615 616 617
  Exceptions : none
  Example    : @dba = @{ Bio::EnsEMBL::Registry
                  ->get_all_DBAdaptors_by_connection($dbc) };
618
  Status     : Stable
619 620 621

=cut

622 623 624
sub get_all_DBAdaptors_by_connection {
  my ( $self, $dbc_orig ) = @_;

625 626
  my @return;

627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661
  foreach my $dba ( @{ $registry_register{'_DBA'} } ) {
    my $dbc = $dba->dbc();

    if (    defined($dbc)
         && $dbc->can('equals')
         && $dbc->equals($dbc_orig) )
    {
      push( @return, $dba );
    }
  }

  return \@return;
}

=head2 get_all_DBAdaptors_by_dbname

  Arg [1]    : string, name of database
  Returntype : reference to list of DBAdaptors
  Exceptions : none
  Example    : @dba = @{ Bio::EnsEMBL::Registry
                  ->get_all_DBAdaptors_by_dbname($dbname) };
  Status     : Stable

=cut

sub get_all_DBAdaptors_by_dbname {
  my ( $self, $dbname ) = @_;

  my @return;

  foreach my $dba ( @{ $registry_register{'_DBA'} } ) {
    my $dbc = $dba->dbc();

    if ( defined($dbc) && $dbc->dbname() eq $dbname ) {
      push( @return, $dba );
662 663
    }
  }
664

665 666 667
  return \@return;
}

668 669 670 671 672 673 674 675 676 677 678
=head2 remove_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->remove_DBAdaptor("Human", "core");
  Returntype : none
  Exceptions : none
  Status     : At risk

=cut

679 680
sub remove_DBAdaptor {
  my ( $class, $species, $group ) = @_;
681 682

  $species = $class->get_alias($species);
683 684

  delete $registry_register{_SPECIES}{$species}{$group};
685
  # This will remove the DBAdaptor and all the other adaptors
686

687
  # Now remove if from the _DBA array
688 689
  my $index;

690
  foreach my $i ( 0 .. $#{ $registry_register{'_DBA'} } ) {
691
    my $dba = $registry_register{'_DBA'}->[$i];
Nathan Johnson's avatar
Nathan Johnson committed
692

693 694 695
    if ( ( $dba->species eq $species )
      && $dba->group eq $group )
    {
696 697 698 699
      $index = $i;
      last;
    }
  }
700

701
  # Now remove from _DBA cache
702 703 704
  if ( defined($index) ) {
    splice( @{ $registry_register{'_DBA'} }, $index, 1 );
  }
Nathan Johnson's avatar
Nathan Johnson committed
705

706
} ## end sub remove_DBAdaptor
707

708

Nathan Johnson's avatar
Nathan Johnson committed
709 710 711 712 713 714 715

=head2 reset_DBAdaptor

  Arg [1]:     string - species e.g. homo_sapiens
  Arg [2]:     string - DB group e.g. core
  Arg [3]:     string - new dbname
  Args [4-7]:  string - optional DB parameters, defaults to current db params if omitted
716
  Arg [8]:     hashref - Hash ref of additional parameters e.g. eFG dnadb params for auto selecting dnadb
717 718
  Usage :      $reg->reset_registry_db( 'homo_sapiens', 'core',
                  'homo_sapiens_core_37_35j' );
Nathan Johnson's avatar
Nathan Johnson committed
719 720 721 722 723 724 725 726
  Description: Resets a DB within the registry.
  Exceptions:  Throws if mandatory params not supplied
               Throws if species name is not already seen by the registry
               Throws if no current DB for species/group available
  Status :     At risk

=cut

727 728 729 730 731
sub reset_DBAdaptor {
  my (
    $self, $species, $group, $dbname, $host,
    $port, $user,    $pass,  $params
  ) = @_;
Nathan Johnson's avatar
Nathan Johnson committed
732

733
  # Check mandatory params
734 735 736 737
  if ( !( defined $species && defined $group && defined $dbname ) ) {
    throw(
      'Must provide at least a species, group, and dbname parameter '
        . 'to redefine a DB in the registry' );
Nathan Johnson's avatar
Nathan Johnson committed
738
  }
739

740
  # Validate species here
Nathan Johnson's avatar
Nathan Johnson committed
741
  my $alias = $self->get_alias($species);
742 743 744
  throw("Could not find registry alias for species:\t$species")
    if ( !defined $alias );

745
  # Get all current defaults if not defined
Nathan Johnson's avatar
Nathan Johnson committed
746

747
  my $db = $self->get_DBAdaptor( $alias, $group );
748
  my $class;
Nathan Johnson's avatar
Nathan Johnson committed
749

750 751 752 753 754 755 756 757 758
  if ($db) {
    $class = ref($db);
    $host ||= $db->dbc->host;
    $port ||= $db->dbc->port;
    $user ||= $db->dbc->username;
    $pass ||= $db->dbc->password;
  } else {
    #Now we need to test mandatory params
    $class = $group2adaptor{ lc($group) };
759

760 761 762 763
    if ( !( $host && $user ) ) {
      throw("No comparable $alias $group DB present in Registry. "
          . "You must pass at least a dbhost and dbuser" );
    }
764
  }
Nathan Johnson's avatar
Nathan Johnson committed
765

766
  $self->remove_DBAdaptor( $alias, $group );
Nathan Johnson's avatar
Nathan Johnson committed
767

768 769 770 771
  #my @adaptors = @{$self->get_all_adaptors};
  #This is causing a loop as it was constantly trying to reset the db
  #and never getting there.
  #I think this was left over from testing
Nathan Johnson's avatar
Nathan Johnson committed
772

773
  # ConfigRegistry should automatically add this to the Registry
774 775

  $db = $class->new(
776 777 778 779 780 781 782 783
    -user    => $user,
    -host    => $host,
    -port    => $port,
    -pass    => $pass,
    -dbname  => $dbname,
    -species => $alias,
    -group   => $group,
    %{$params} );
Nathan Johnson's avatar
Nathan Johnson committed
784 785

  return $db;
786
} ## end sub reset_DBAdaptor
Nathan Johnson's avatar
Nathan Johnson committed
787 788


Ian Longden's avatar
Ian Longden committed
789 790 791 792 793 794 795 796
#
# 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.
797 798 799
  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
800 801
  Returntype : none
  Exceptions : none
802
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
803 804 805

=cut

806 807
sub add_DNAAdaptor {
  my ( $class, $species, $group, $dnadb_species, $dnadb_group ) = @_;
Ian Longden's avatar
Ian Longden committed
808

809
  $species       = $class->get_alias($species);
810
  $dnadb_species = $class->get_alias($dnadb_species);
811
  if ( $dnadb_group->isa('Bio::EnsEMBL::DBSQL::DBAdaptor') ) {
Ian Longden's avatar
Ian Longden committed
812
    deprecated("");
813
  } else {
814 815 816
    $registry_register{_SPECIES}{$species}{ lc($group) }{'_DNA'} =
      $dnadb_group;
    $registry_register{_SPECIES}{$species}{ lc($group) }{'_DNA2'} =
817
      $dnadb_species;
818
  }
Ian Longden's avatar
Ian Longden committed
819 820 821 822 823 824 825 826 827
}

=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
828
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
829 830 831

=cut

832 833
sub get_DNAAdaptor {
  my ( $class, $species, $group ) = @_;
Ian Longden's avatar
Ian Longden committed
834 835

  $species = $class->get_alias($species);
836 837 838 839
  my $new_group =
    $registry_register{_SPECIES}{$species}{ lc($group) }{'_DNA'};
  my $new_species =
    $registry_register{_SPECIES}{$species}{ lc($group) }{'_DNA2'};
840 841 842

  if ( defined $new_group ) {
    return $class->get_DBAdaptor( $new_species, $new_group );
843
  }
844 845

  return undef;
Ian Longden's avatar
Ian Longden committed
846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861
}

#
# 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
862 863
  Caller     : internal
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
864 865 866

=cut

867 868
sub add_adaptor {
  my ( $class, $species, $group, $type, $adap, $reset ) = @_;
Ian Longden's avatar
Ian Longden committed
869 870 871

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

872 873 874 875 876
  # Since the adaptors are not stored initially, only their 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
Ian Longden's avatar
Ian Longden committed
877

878 879
  if ( defined($reset) )
  {    # JUST REST THE HASH VALUE NO MORE PROCESSING NEEDED
880 881
    $registry_register{_SPECIES}{$species}{ lc($group) }{ lc($type) } =
      $adap;
Ian Longden's avatar
Ian Longden committed
882 883
    return;
  }
884

885
  if (
886 887 888
    defined(
      $registry_register{_SPECIES}{$species}{ lc($group) }{ lc($type) }
    ) )
889 890 891
  {
  # print STDERR (
  #      "Overwriting Adaptor in Registry for $species $group $type\n");
892 893
    $registry_register{_SPECIES}{$species}{ lc($group) }{ lc($type) } =
      $adap;
894
    return;
Ian Longden's avatar
Ian Longden committed
895
  }
896 897
  $registry_register{_SPECIES}{$species}{ lc($group) }{ lc($type) } =
    $adap;
Ian Longden's avatar
Ian Longden committed
898

899 900
  if ( !defined( $registry_register{_SPECIES}{$species}{'list'} ) ) {
    $registry_register{_SPECIES}{$species}{'list'} = [$type];
901
  } else {
902
    push( @{ $registry_register{_SPECIES}{$species}{'list'} }, $type );
Ian Longden's avatar
Ian Longden committed
903 904
  }

905 906
  if ( !defined( $registry_register{_TYPE}{ lc($type) }{$species} ) ) {
    $registry_register{_TYPE}{ lc($type) }{$species} = [$type];
907
  } else {
908 909
    push( @{ $registry_register{_TYPE}{ lc($type) }{$species} },
      $adap );
Ian Longden's avatar
Ian Longden committed
910 911
  }

912
} ## end sub add_adaptor
Ian Longden's avatar
Ian Longden committed
913 914 915 916 917 918 919 920 921 922


=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
923
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
924 925 926

=cut

927 928
sub get_adaptor {
  my ( $class, $species, $group, $type ) = @_;
Glenn Proctor's avatar
Typos.  
Glenn Proctor committed
929

930
  $species = $class->get_alias($species);
Glenn Proctor's avatar
Typos.  
Glenn Proctor committed
931

932 933 934 935 936 937 938 939
  my %dnadb_adaptors = (
    'sequence'                 => 1,
    'assemblymapper'           => 1,
    'karyotypeband'            => 1,
    'repeatfeature'            => 1,
    'coordsystem'              => 1,
    'assemblyexceptionfeature' => 1
  );
940

941
  ## warn "$species, $group, $type";
942 943 944

  $type = lc($type);

945 946
  my $dnadb_group =
    $registry_register{_SPECIES}{$species}{ lc($group) }{'_DNA'};
947

948 949 950
  if ( defined($dnadb_group)
    && defined( $dnadb_adaptors{ lc($type) } ) )
  {
951 952 953
    $species =
      $registry_register{_SPECIES}{$species}{ lc($group) }{'_DNA2'};
    $group = $dnadb_group;
Ian Longden's avatar
Ian Longden committed
954 955
  }

956 957 958
  my $ret =
    $registry_register{_SPECIES}{$species}{ lc($group) }{ lc($type) };

959 960
  if ( !defined($ret) ) { return undef }
  if ( ref($ret) )      { return $ret }
961

962
  # Not instantiated yet
Ian Longden's avatar
Ian Longden committed
963

964
  my $dba = $registry_register{_SPECIES}{$species}{ lc($group) }{'_DB'};
965 966 967 968 969 970
  my $module = $ret;

  eval "require $module";
  if ($@) {
    warning("'$module' cannot be found.\nException $@\n");
    return undef;
Ian Longden's avatar
Ian Longden committed
971 972
  }

973
  if (
974 975 976
    !defined(
      $registry_register{_SPECIES}{$species}{ lc($group) }{'CHECKED'} )
    )
977
  {
978
    $registry_register{_SPECIES}{$species}{ lc($group) }{'CHECKED'} = 1;
979 980 981 982 983 984 985 986
    $class->version_check($dba);
  }

  my $adap = "$module"->new($dba);
  Bio::EnsEMBL::Registry->add_adaptor( $species, $group, $type, $adap,
    'reset' );
  $ret = $adap;

Ian Longden's avatar
Ian Longden committed
987
  return $ret;
988
} ## end sub get_adaptor
Ian Longden's avatar
Ian Longden committed
989 990 991

=head2 get_all_adaptors

992 993 994 995 996 997
  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
998
  Example    : @adaps = @{Bio::EnsEMBL::Registry->get_all_adaptors()};
999
  Returntype : ref to list of adaptors
Ian Longden's avatar
Ian Longden committed
1000
  Exceptions : none
1001
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
1002 1003 1004 1005

=cut

sub get_all_adaptors{
1006 1007 1008 1009
  my ($class,@args)= @_;
  my ($species, $group, $type);
  my @ret=();
  my (%species_hash, %group_hash, %type_hash);