Registry.pm 69 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 vars qw(%registry_register);

122
my $API_VERSION = 51;
Ian Longden's avatar
Ian Longden committed
123
124

=head2 load_all
125

126
127
128
129
130
131
132
133
 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
134

135
136
  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
137

138
139
140
141
142
143
144
145
  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).
146
147
148
149
150
151
152
  Arg [4]:     (optional) int 1
               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
153
154
155
  Example    : Bio::EnsEMBL::Registry->load_all();
  Returntype : none
  Exceptions : none
156
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
157
158

=cut
159

160
161
sub load_all {
    my $class = shift;
162
    my ( $config_file, $verbose, $no_clear, $no_cache ) = @_;
163
164
165
166
167
168

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

    $verbose  ||= 0;
    $no_clear ||= 0;
169
    $no_cache ||= 0;
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
195
196
197
198
199

    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 );
        }

200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
        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 );
        }
216

217
        if ( defined $cfg ) {
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
            # 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
243
244
245
246
247
248
249
250
251
252
253
254
255
                # 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 ) ]
                    );
256
                }
257

258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
                %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;
                }

289
290
291
292
293
                # 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.

294
295
296
                my $alias = $cfg->val( $section, 'alias' );
                $cfg->delval( $section, 'alias' );

297
298
299
300
301
302
303
304
305
306
307
                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.
308
309
310
311
312
                # 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, $parameter );
313
314
315
316
		    #when set, do not use the feature cache in the different adaptors
		    if ($no_cache){
			$adaptor_args{'-no_cache'} = 1;
		    }
317
318
319
320
321
322
323
324
                }

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

325
326
327
                eval "require $adaptor";
                if ($@) { die($@) }

328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
                $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...
343
} ## end sub load_all
344
345

=head2 clear
346

347
348
349
350
351
 Will clear the registry and disconnect from all databases.

  Example    : Bio::EnsEMBL::Registry->clear();
  Returntype : none
  Exceptions : none
352
  Status     : Stable
353
354
355
356
357
358
359
360
361
362
363

=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
364
  %registry_register = ();
Ian Longden's avatar
Ian Longden committed
365
366
367
}

#
368
# db adaptors. (for backwards compatibility)
Ian Longden's avatar
Ian Longden committed
369
370
371
372
#

=head2 add_db

373
  Arg [1]    : db (DBAdaptor) to add adaptor to.
Ian Longden's avatar
Ian Longden committed
374
375
376
377
378
  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
379
  Status     : At Risk.
380
             : This is here for backwards compatibility only and may be removed 
381
382
383
             : 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
384
385
386
387
388
389
=cut

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


390
391
  if(lc($db->species()) ne lc($adap->species)){
    $registry_register{lc($db->species())}{lc($db->group())}{'_special'}{lc($name)} = $adap;
392
  }
Ian Longden's avatar
Ian Longden committed
393
394
395
396
}

=head2 remove_db

397
  Arg [1]    : db (DBAdaptor) to remove adaptor from.
Ian Longden's avatar
Ian Longden committed
398
399
400
401
  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
402
  Status     : At Risk.
403
             : This is here for backwards compatibility only and may be removed 
404
405
             : 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
406
407
408
409
410
411

=cut

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

412
413
  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
414
415
416
417
418
419

  return $ret;
}

=head2 get_db

420
  Arg [1]    : db (DBAdaptor) to get adaptor from.
Ian Longden's avatar
Ian Longden committed
421
422
423
424
  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
425
  Status     : At Risk.
426
             : This is here for backwards compatibility only and may be removed 
427
428
             : 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
429
430
431
432
433
434

=cut

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

435
  my $ret = Bio::EnsEMBL::Registry->get_DBAdaptor(lc($db->species),lc($name));
436
437
438
439

  if(defined($ret)){
    return $ret;
  }
440
  return $registry_register{lc($db->species())}{lc($db->group())}{'_special'}{lc($name)};
Ian Longden's avatar
Ian Longden committed
441
442
443
444
}

=head2 get_all_db_adaptors

445
  Arg [1]    : db (DBAdaptor) to get all the adaptors from.
Ian Longden's avatar
Ian Longden committed
446
447
448
  Example    : my $db = Bio::EnsEMBL::Registry->get_all_db_adaptors($db);
  Returntype : adaptor
  Exceptions : none
449
  Status     : At Risk.
450
             : This is here for backwards compatibility only and may be removed 
451
452
453
             : 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
454
455
456

=cut

457
458
459
sub get_all_db_adaptors {
  my ( $class, $db ) = @_;
  my %ret = ();
Ian Longden's avatar
Ian Longden committed
460

461
462
  # 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
463

464
465
466
467
  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
468
469
  }

470
471
472
473
474
475
476
477
478
  foreach my $key (
             keys %{
               $registry_register{ $class->get_alias( $db->species() ) }
                 { lc( $db->group() ) }{'_special'} } )
  {
    $ret{$key} =
      $registry_register{ $class->get_alias( $db->species() ) }
      { lc( $db->group() ) }{'_special'}{$key};
  }
Ian Longden's avatar
Ian Longden committed
479
480

  return \%ret;
481
} ## end sub get_all_db_adaptors
Ian Longden's avatar
Ian Longden committed
482
483
484
485
486
487
488
489
490
491
492
493
494
495


#
# 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
496
497
  caller     : internal
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
498
499
500
501
502
503

=cut

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

504
505
506
507
508
  if(!($class->alias_exists($species))){
    $class->add_alias($species,$species);
  }
  

Ian Longden's avatar
Ian Longden committed
509
510
  $species = $class->get_alias($species);

511
  $registry_register{$species}{lc($group)}{'_DB'} = $adap;
Ian Longden's avatar
Ian Longden committed
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532

  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
533
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
534
535
536
537
538
539
540
541

=cut

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

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

542
543
  return  $registry_register{$species}{lc($group)}{'_DB'};

Ian Longden's avatar
Ian Longden committed
544
545
546
547
}

=head2 get_all_DBAdaptors

548
549
550
551
552
553
554
555
  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
556
  Status       : Stable
Ian Longden's avatar
Ian Longden committed
557
558
559
560

=cut

sub get_all_DBAdaptors{
561
562
  my ($class,@args)=@_;
  my @ret;
Ian Longden's avatar
Ian Longden committed
563

564
565
566
567
568
569
  my ($species, $group) = 
    rearrange([qw(SPECIES GROUP)], @args);
  if(defined($species)){
    $species = $class->get_alias($species);
  }
  foreach my $dba (@{$registry_register{'_DBA'}}){
570
    if(!defined($species) || lc($species) eq lc($dba->species)){
571
572
573
574
575
576
577
578
      if(!defined($group) || lc($group) eq lc($dba->group)){
	push @ret, $dba;
      }
    }
  }


  return \@ret;
Ian Longden's avatar
Ian Longden committed
579
580
}

581
582
583
584
585
586
=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);
587
  Status     : Stable
588
589
590
591
592
593
594
595
596

=cut

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

  foreach my $dba ( @{$registry_register{'_DBA'}}){
    my $dbc = $dba->dbc;
Web Admin's avatar
Web Admin committed
597
    if($dbc && $dbc->can('equals') && $dbc->equals($dbc_orig)){
598
599
600
601
602
603
      push @return, $dba;
    }
  }
  return \@return;
}

604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
=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

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

  $species = $class->get_alias($species);
Nathan Johnson's avatar
Nathan Johnson committed
619
620
  
 
621
  delete $registry_register{$species}{$group};
622
  # This will remove the DBAdaptor and all the other adaptors
623

624
  # Now remove if from the _DBA array
625
626
  my $index;

Nathan Johnson's avatar
Nathan Johnson committed
627

628
629
  foreach my $i(0..$#{$registry_register{'_DBA'}}){
    my $dba = $registry_register{'_DBA'}->[$i];
Nathan Johnson's avatar
Nathan Johnson committed
630

631
632
633
    if(($dba->species eq $species) &&
       $dba->group eq $group){
      $index = $i;
Nathan Johnson's avatar
Nathan Johnson committed
634

635
636
637
638
      last;
    }
  }
  
639
  # Now remove from _DBA cache
Nathan Johnson's avatar
Nathan Johnson committed
640
641
  splice(@{$registry_register{'_DBA'}}, $index, 1);

642
643
644
  return;
}

645

Nathan Johnson's avatar
Nathan Johnson committed
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664

=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
  Usage :      $reg->reset_registry_db('homo_sapiens', 'core', 'homo_sapiens_core_37_35j');
  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

sub reset_DBAdaptor{
  my ($self, $species, $group, $dbname, $host, $port, $user, $pass) = @_;

665
  # Check mandatory params
Nathan Johnson's avatar
Nathan Johnson committed
666
667
668
669
  if(! (defined $species && defined $group && defined $dbname)){
	throw('Must provide at least a species, group and dbname parmeter to redefine a DB in the registry');
  }
  
670
  # Validate species here
Nathan Johnson's avatar
Nathan Johnson committed
671
672
673
674
  my $alias = $self->get_alias($species);
  throw("Could not find registry alias for species:\t$species") if(! defined $alias);
 

675
  # Get all current defaults if not defined
Nathan Johnson's avatar
Nathan Johnson committed
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
  my $current_db = $self->get_DBAdaptor($alias, $group);
  
  if(! defined $current_db){
	throw("There is not current registry DB for:\t${alias}\t${group}");
  }


  $host ||= $current_db->dbc->host;
  $port ||= $current_db->dbc->port;
  $user ||= $current_db->dbc->username;
  $pass ||= $current_db->dbc->password;
  my $class = ref($current_db);

  $self->remove_DBAdaptor($alias, $group);
  
Nathan Johnson's avatar
Nathan Johnson committed
691
692
  my @adaptors = @{$self->get_all_adaptors};

Nathan Johnson's avatar
Nathan Johnson committed
693

694
  # ConfigRegistry should automatically add this to the Registry
Nathan Johnson's avatar
Nathan Johnson committed
695
696
697
698
699
700
701
702
703
704
705
706
707
708
  my $db = $class->new(
					   -user => $user,
					   -host => $host,
					   -port => $port,
					   -pass => $pass,
					   -dbname => $dbname,
					   -species => $alias,
					   -group    => $group,
					  );

  return $db;
}


Ian Longden's avatar
Ian Longden committed
709
710
711
712
713
714
715
716
#
# 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.
717
718
719
  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
720
721
  Returntype : none
  Exceptions : none
722
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
723
724
725
726

=cut

sub add_DNAAdaptor{
Ian Longden's avatar
Ian Longden committed
727
  my ($class, $species, $group, $dnadb_species, $dnadb_group) = @_;
Ian Longden's avatar
Ian Longden committed
728
729

  $species = $class->get_alias($species);
730
  $dnadb_species = $class->get_alias($dnadb_species);
731
  if($dnadb_group->isa('Bio::EnsEMBL::DBSQL::DBAdaptor')){
Ian Longden's avatar
Ian Longden committed
732
    deprecated("");
733
734
  }
  else{
735
736
    $registry_register{$species}{lc($group)}{'_DNA'} = $dnadb_group;
    $registry_register{$species}{lc($group)}{'_DNA2'} = $dnadb_species;
737
  }
Ian Longden's avatar
Ian Longden committed
738
739
740
741
742
743
744
745
746
}

=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
747
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
748
749
750
751
752
753
754

=cut

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

  $species = $class->get_alias($species);
755
756
  my $new_group = $registry_register{$species}{lc($group)}{'_DNA'};
  my $new_species = $registry_register{$species}{lc($group)}{'_DNA2'};
757
  if( defined $new_group ) {
Ian Longden's avatar
Ian Longden committed
758
    return  $class->get_DBAdaptor($new_species,$new_group);
759
760
761
  } else {
    return undef;
  }
Ian Longden's avatar
Ian Longden committed
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
}

#
# 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
778
779
  Caller     : internal
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
780
781
782
783


=cut

784
785
sub add_adaptor {
  my ( $class, $species, $group, $type, $adap, $reset ) = @_;
Ian Longden's avatar
Ian Longden committed
786
787
788

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

789
790
791
792
793
  # 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
794

795
796
797
  if ( defined($reset) )
  {    # JUST REST THE HASH VALUE NO MORE PROCESSING NEEDED
    $registry_register{$species}{ lc($group) }{ lc($type) } = $adap;
Ian Longden's avatar
Ian Longden committed
798
799
    return;
  }
800
801
802
803
804
805
806
  if (
    defined( $registry_register{$species}{ lc($group) }{ lc($type) } ) )
  {
  # print STDERR (
  #      "Overwriting Adaptor in Registry for $species $group $type\n");
    $registry_register{$species}{ lc($group) }{ lc($type) } = $adap;
    return;
Ian Longden's avatar
Ian Longden committed
807
  }
808
  $registry_register{$species}{ lc($group) }{ lc($type) } = $adap;
Ian Longden's avatar
Ian Longden committed
809

810
811
812
813
  if ( !defined( $registry_register{$species}{'list'} ) ) {
    $registry_register{$species}{'list'} = [$type];
  } else {
    push( @{ $registry_register{$species}{'list'} }, $type );
Ian Longden's avatar
Ian Longden committed
814
815
  }

816
817
818
819
  if ( !defined( $registry_register{ lc($type) }{$species} ) ) {
    $registry_register{ lc($type) }{$species} = [$type];
  } else {
    push( @{ $registry_register{ lc($type) }{$species} }, $adap );
Ian Longden's avatar
Ian Longden committed
820
821
  }

822
} ## end sub add_adaptor
Ian Longden's avatar
Ian Longden committed
823
824
825
826
827
828
829
830
831
832


=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
833
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
834
835
836
837
838

=cut

sub get_adaptor{
  my ($class,$species,$group,$type)= @_;
Glenn Proctor's avatar
Typos.  
Glenn Proctor committed
839

840
  $species = $class->get_alias($species);
Glenn Proctor's avatar
Typos.  
Glenn Proctor committed
841

842
  my %dnadb_adaptors = qw(sequence  1 assemblymapper 1  karyotypeband 1 repeatfeature 1 coordsystem 1  assemblyexceptionfeature 1 );
843

844
  my $dnadb_group =  $registry_register{$species}{lc($group)}{_DNA};
845

846
847
  if( defined($dnadb_group) && defined($dnadb_adaptors{lc($type)}) ) {
      $species = $registry_register{$species}{lc($group)}{'_DNA2'};
848
      $group = $dnadb_group;
Ian Longden's avatar
Ian Longden committed
849
850
  }

851
852
853
  my $ret = $registry_register{$species}{ lc($group) }{ lc($type) };
  if ( !defined($ret) ) { return undef; }

Ian Longden's avatar
Ian Longden committed
854
  if(!ref($ret)){ # not instantiated yet
855
    my $dba = $registry_register{$species}{lc($group)}{'_DB'};
Ian Longden's avatar
Ian Longden committed
856
857
858
859
860
861
862
    my $module = $ret;
    eval "require $module";

    if($@) {
      warning("$module cannot be found.\nException $@\n");
      return undef;
    }
863
864
865
866
    if(!defined($registry_register{$species}{lc($group)}{'CHECKED'})){
      $registry_register{$species}{lc($group)}{'CHECKED'} = 1;
      $class->version_check($dba);
    }
Ian Longden's avatar
Ian Longden committed
867
868
869
870
871
872
873
874
875
876
    my $adap = "$module"->new($dba);
    Bio::EnsEMBL::Registry->add_adaptor($species, $group, $type, $adap, "reset");
    $ret = $adap;
  }

  return $ret;
}

=head2 get_all_adaptors

877
878
879
880
881
882
  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
883
  Example    : @adaps = @{Bio::EnsEMBL::Registry->get_all_adaptors()};
884
  Returntype : ref to list of adaptors
Ian Longden's avatar
Ian Longden committed
885
  Exceptions : none
886
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
887
888
889
890

=cut

sub get_all_adaptors{
891
892
893
894
  my ($class,@args)= @_;
  my ($species, $group, $type);
  my @ret=();
  my (%species_hash, %group_hash, %type_hash);
Ian Longden's avatar
Ian Longden committed
895

896

897
  if(@args == 1){ # Old species only one parameter
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
    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'}}){ 
929
	foreach my $ty (@{$registry_register{lc($dba->species)}{'list'}}){
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
	  $type_hash{lc($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
947
948
949
950
951
952
953
954
955
956
957
}


=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
958
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
959
960
961
962
963
964

=cut

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

965
  $registry_register{'_ALIAS'}{lc($key)} = lc($species);
Ian Longden's avatar
Ian Longden committed
966
967
968
969
970
971
972
973
}

=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
974
  Exceptions : none
975
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
976
977
978
979

=cut

sub get_alias{
980
  my ($class, $key) = @_;
Ian Longden's avatar
Ian Longden committed
981

982
  if(!defined($registry_register{'_ALIAS'}{lc($key)})){
983
    return $key;
Ian Longden's avatar
Ian Longden committed
984
  }
985
  return $registry_register{'_ALIAS'}{lc($key)};
Ian Longden's avatar
Ian Longden committed
986
}
987
988
989
990

=head2 alias_exists

  Arg [1]    : name of the possible alias to get species for
Ian Longden's avatar
Ian Longden committed
991
  Example    : Bio::EnsEMBL::Registry->alias_exists("Human");
992
993
994
  Description: does the species name exist.
  Returntype : 1 if exists else 0
  Exceptions : none
995
  Status     : Stable
996
997
998
999
1000
1001

=cut

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

1002
  if(defined($registry_register{'_ALIAS'}{lc($key)})){
1003
1004
1005
1006
    return 1;
  }
  return 0;
}
1007

1008
1009
1010
1011
1012
1013
1014
=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
1015
  Status     : Stable
1016
1017
1018

=cut

1019
sub set_disconnect_when_inactive{
1020
  foreach my $dba ( @{get_all_DBAdaptors()}){
1021
    my $dbc = $dba->dbc;
1022
    # Disconnect if connected
1023
    $dbc->disconnect_if_idle() if $dbc->connected();
1024
1025
1026
    $dbc->disconnect_when_inactive(1);
  }
}
Ian Longden's avatar
Ian Longden committed
1027

1028
1029
1030
1031
1032
1033
1034

=head2 disconnect_all

  Example    : Bio::EnsEMBL::Registry->disconnect_all();
  Description: disconnect from all the databases.
  Returntype : none
  Exceptions : none
1035
  Status     : Stable
1036
1037
1038

=cut

1039
sub disconnect_all {
Web Admin's avatar
fixed  
Web Admin committed
1040
  foreach my $dba ( @{get_all_DBAdaptors()||[]} ){
1041
    my $dbc = $dba->dbc;
Web Admin's avatar
Web Admin committed
1042
    next unless $dbc;
1043
    # Disconnect if connected
1044
1045
1046
    $dbc->disconnect_if_idle() if $dbc->connected();
  }
}
1047

1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
=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
1066
  Status     : Stable
1067
1068
1069
1070

=cut

sub change_access{
Steve Trevanion's avatar
Steve Trevanion committed
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
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);
	}
1087
1088
1089
    }
}

1090
1091


1092
1093
=head2 load_registry_from_url

Glenn Proctor's avatar
Typos.  
Glenn Proctor committed
1094
  Arg [1] : string $url
1095
1096
1097
1098
1099
1100
1101
1102
1103
  Arg [2] : (optional) integer
               If not 0, will print out all information.
  Arg [3] : (optional) integer
               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           
Glenn Proctor's avatar
Typos.  
Glenn Proctor committed
1104
  Example : load_registry_from_url(mysql://anonymous@ensembldb.ensembl.org:3306);
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
  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 {
1118
  my ($self, $url, $verbose, $no_cache) = @_;
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137

  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,
1138
1139
        -verbose => $verbose,
	-no_cache => $no_cache);
1140
1141
1142
1143
1144
1145
  } else {
    throw("Only MySQL URLs are accepted at the moment");
  }
}


1146
=head2 load_registry_from_db
1147

1148
1149
1150
1151
1152
1153
1154
1155
1156
  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 
1157
1158
1159
1160
1161
1162
  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.
1163
1164
1165
1166
1167
  Arg [WAIT_TIMEOUT]: (optional) integer
                 Time in seconds for the wait timeout to happen. Time after which
                 the connection is deleted if not used. By default this is 28800 (8 hours)
                 So set this to greater than this if your connection are getting deleted.
                 Only set this if you are having problems and know what you are doing.
1168
1169
1170
1171
1172
1173
1174
   Arg [-NO_CACHE]: (optional) int 1
                 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       
1175
1176
1177
1178
1179

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

1180
  Description: Will load the correct versions of the ensembl databases for the
1181
               software release it can find on a database instance into the 
1182
               registry. Also adds a set of standard aliases.
1183
1184

  Exceptions : None.
1185
  Status     : Stable
1186
1187
 
=cut
1188

1189
sub load_registry_from_db {
1190
1191
1192
  my ( $self, @args ) = @_;

  my ( $host, $port, $user, $pass, $verbose, $db_version,
1193
       $wait_timeout, $no_cache ) =
1194
    rearrange(
1195
             [qw(HOST PORT USER PASS VERBOSE DB_VERSION WAIT_TIMEOUT NO_CACHE)],
1196
             @args );
1197
1198
1199

  my $go_version = 0;
  my $compara_version =0;
1200
  my $ancestral_version =0;
1201
1202

  $user ||= "ensro";
1203
1204
1205
1206
1207
  if ( !defined($port) ) {
    $port = 3306;
    if ( $host eq "ensembldb.ensembl.org" ) {
      if ( !defined($db_version) or $db_version >= 48 ) {
        $port = 5306;
1208
1209
1210
1211
      }
    }
  }

1212
  $wait_timeout ||= 0;
1213

1214
1215
1216
1217
1218
  my $dbh =
    DBI->connect( "DBI:mysql:host=$host;port=$port", $user, $pass );

  my $res = $dbh->selectall_arrayref("show databases");
  my @dbnames = map { $_->[0] } @$res;
1219

1220
  my %temp;
1221
  my $software_version = $self->software_version();
1222
1223

  if ( defined($db_version) ) {
1224
1225
    $software_version = $db_version;
  }
1226
1227
1228
1229
1230
1231

  if ($verbose) {
    printf( "Will only load v%d databases\n", $software_version );
  }

  for my $db (@dbnames) {
1232
    if ( $db =~ /^(\w+)_(collection_core_(?:\d+_)?(\d+)_(\w+))/ )
1233
1234
    {    # NEEDS TO BE FIRST
      if ( $3 eq $software_version ) {
1235
        $temp{$1} = $2;
1236
      }
1237
1238
1239
    } elsif ( $db =~ /^([a-z]+_[a-z]+_[a-z]+)_(\d+)_(\d+[a-z]*)/ ) {
      if ( $2 eq $software_version ) {
        $temp{$1} = $2 . "_" . $3;
1240
      }
1241
1242
1243
1244
1245
    } elsif ( $db =~ /^(.+)_(userdata)$/ ) {
      $temp{$1} = $2;
    } elsif ( $db =~ /^ensembl_compara_(\d+)/ ) {
      if ( $1 eq $software_version ) {
        $compara_version = $1;
1246
      }
1247
1248
1249
1250
1251
1252
1253
    } elsif ( $db =~ /^ensembl_ancestral_(\d+)/ ) {
      if ( $1 eq $software_version ) {
        $ancestral_version = $1;
      }
    } elsif ( $db =~ /^ensembl_go_(\d+)/ ) {
      if ( $1 eq $software_version ) {
        $go_version = $1;
1254
1255
      }
    }
1256
1257
1258
1259
1260
1261
  } ## end for my $db (@dbnames)

  @dbnames = ();

  foreach my $key ( keys %temp ) {
    push @dbnames, $key . "_" . $temp{$key};
1262
  }
1263
1264
1265

  # Register Core databases

1266
  my @core_dbs = grep { /^[a-z]+_[a-z]+_core_\d+_/ } @dbnames;
1267
1268

  foreach my $coredb (@core_dbs) {
1269
1270
    next if ($coredb =~ /collection/);  # Skip multi-species databases

1271
1272
1273
1274
1275
1276
1277
1278
1279
1280
1281
    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