Registry.pm 35.1 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 18
Bio::EnsEMBL::Registry->load_all("configuration_file");

$gene_adaptor = Bio::EnsEMBL::Registry->get_adaptor("homo_sapiens","core","gene"))
Ian Longden's avatar
Ian Longden committed
19 20 21 22 23 24 25


=head1 DESCRIPTION

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 29 30 31 32
The registry can be loaded from a configuration file using the method load_all.
If a file is passed to load_all then this is used.
Else if the enviroment variable ENSEMBL_REGISTRY is set then this is used
Else if the file .ensembl_init in your home directory exist it is used.

For the Web server ENSEMBL_REGISTRY should be set in SiteDefs.pm, which will
pass this on to load_all.
Ian Longden's avatar
Ian Longden committed
33

34 35 36 37

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

Ian Longden's avatar
Ian Longden committed
38 39 40 41 42 43
The four types of registrys are for db adaptors, dba adaptors, dna adaptors
and the standard type.

=head2 db

These are registrys for backwards compatibillity and enable the subroutines
44
to add other adaptors to connections. 
Ian Longden's avatar
Ian Longden committed
45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73

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
   my $sfa = $self->adaptor()->db()->get_db_adaptor('blast');

We now want to change this to
   my $sfa = Bio::EnsEMBL::Registry->get_adaptor("Human","core","blast");


=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

my $db = Bio::EnsEMBL::DBSQL::DBAdaptor->new(....)
my $exon_adaptor = $db->get_ExonAdaptor;

we should now have just

my  $exon_adaptor = Bio::EnsEMBL::Registry->get_adaptor("Human","core","Exon");


=head2 DNA

This is an internal Registry and allows the configuration of a dnadb. 
Steve Trevanion's avatar
Steve Trevanion committed
74
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
75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103

## set the est db to use the core for getting dna data.
#Bio::EnsEMBL::Utils::ConfigRegistry->
#                         dnadb_add("Homo Sapiens","core","Homo Sapiens","est");


=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.

my  $exon_adaptor = Bio::EnsEMBL::Registry->get_adaptor("Human","core","Exon");

=head1 CONTACT

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


=head1 METHODS

=cut


package Bio::EnsEMBL::Registry;

use strict;

104
use Bio::EnsEMBL::DBSQL::DBAdaptor;
Ian Longden's avatar
Ian Longden committed
105 106
use Bio::EnsEMBL::Utils::Exception qw( deprecate throw warning );
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
107
use Bio::EnsEMBL::Utils::ConfigRegistry;
108
use DBI;
Ian Longden's avatar
Ian Longden committed
109 110 111

use vars qw(%registry_register);

112
my $API_VERSION = 36;
113

Ian Longden's avatar
Ian Longden committed
114 115

=head2 load_all
116

Ian Longden's avatar
Ian Longden committed
117 118 119 120 121 122 123 124
 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 conf file.
  2) If the enviroment variable ENSEMBL_REGISTRY is set this is used.
  3) If the file .ensembl_init exist in the home directory it is used

  Arg [1]    : (optional) string $arg file to load the registry from
125
  Arg [2]    : (optional) string if set prints out messages about conf file used.
Ian Longden's avatar
Ian Longden committed
126 127 128
  Example    : Bio::EnsEMBL::Registry->load_all();
  Returntype : none
  Exceptions : none
129
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
130 131 132 133

=cut
 
sub load_all{
134
  my $class = shift;
135
  my $conf_file = shift;
136
  my $verbose = shift;
137 138
  
  if(defined($registry_register{'seen'})){
139
    print STDERR "Clearing previuosly loaded configuration from Registry\n" if ($verbose);
140 141 142
    $class->clear();
  }
  $registry_register{'seen'}=1;
143
  if(defined($conf_file)){
144 145
    print STDERR  "Loading conf from site defs file ".$conf_file."\n" if ($verbose);
;
146
    if(-e $conf_file){
147 148
      eval{ require($conf_file) }; $@ && die($@);
      
149
      # other wise it gets done again by the web initialisation stuff
150
      delete $INC{$conf_file}; 
151
    }
Ian Longden's avatar
Ian Longden committed
152 153 154
    else{ #error message
      print STDERR "File passed (".$conf_file.") does not exist therefore no configuration loaded\n";
    }
155 156 157
  }
  elsif(defined($ENV{ENSEMBL_REGISTRY}) and -e $ENV{ENSEMBL_REGISTRY}){
    my $file = $ENV{ENSEMBL_REGISTRY};
158 159 160
    print STDERR  "Loading conf from ".$file."\n"  if ($verbose);
;
    eval{ require($file) }; $@ && die($@);
161 162 163 164
  }
  elsif(-e $ENV{HOME}."/.ensembl_init") {
    my $file = $ENV{HOME}."/.ensembl_init";
    
165
    eval{ require($file) }; $@ && die($@)
166 167
  }
  else{
168
    print STDERR "NO default configuration to load\n" if ($verbose);
169 170 171 172 173
  }
}


=head2 clear
174

175 176 177 178 179
 Will clear the registry and disconnect from all databases.

  Example    : Bio::EnsEMBL::Registry->clear();
  Returntype : none
  Exceptions : none
180
  Status     : Stable
181 182 183 184 185 186 187 188 189 190 191

=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
192
  %registry_register = ();
Ian Longden's avatar
Ian Longden committed
193 194 195
}

#
196
# db adaptors. (for backwards compatibillity)
Ian Longden's avatar
Ian Longden committed
197 198 199 200
#

=head2 add_db

201
  Arg [1]    : db (DBAdaptor) to add adaptor to.
Ian Longden's avatar
Ian Longden committed
202 203 204 205 206
  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
207 208 209 210 211
  Status     : At Risk.
             : This is here for backwards compatibillity 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
212 213 214 215 216 217
=cut

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


218 219
  if(lc($db->species()) ne lc($adap->species)){
    $registry_register{lc($db->species())}{lc($db->group())}{'_special'}{lc($name)} = $adap;
220
  }
Ian Longden's avatar
Ian Longden committed
221 222 223 224
}

=head2 remove_db

225
  Arg [1]    : db (DBAdaptor) to remove adaptor from.
Ian Longden's avatar
Ian Longden committed
226 227 228 229
  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
230 231 232 233
  Status     : At Risk.
             : This is here for backwards compatibillity 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
234 235 236 237 238 239

=cut

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

240 241
  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
242 243 244 245 246 247

  return $ret;
}

=head2 get_db

248
  Arg [1]    : db (DBAdaptor) to get adaptor from.
Ian Longden's avatar
Ian Longden committed
249 250 251 252
  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
253 254 255 256
  Status     : At Risk.
             : This is here for backwards compatibillity 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
257 258 259 260 261 262

=cut

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

263
  my $ret = Bio::EnsEMBL::Registry->get_DBAdaptor(lc($db->species),lc($name));
264 265 266 267

  if(defined($ret)){
    return $ret;
  }
268
  return $registry_register{lc($db->species())}{lc($db->group())}{'_special'}{lc($name)};
Ian Longden's avatar
Ian Longden committed
269 270 271 272
}

=head2 get_all_db_adaptors

273
  Arg [1]    : db (DBAdaptor) to get all the adaptors from.
Ian Longden's avatar
Ian Longden committed
274 275 276
  Example    : my $db = Bio::EnsEMBL::Registry->get_all_db_adaptors($db);
  Returntype : adaptor
  Exceptions : none
277 278 279 280 281
  Status     : At Risk.
             : This is here for backwards compatibillity 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");

Ian Longden's avatar
Ian Longden committed
282 283 284 285 286 287 288

=cut

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

Ian Longden's avatar
Ian Longden committed
289 290 291 292
# 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'}}){
293
    if(lc($dba->species()) eq lc($db->species())){
Ian Longden's avatar
Ian Longden committed
294 295 296 297
      $ret{$dba->group()} = $dba;
    } 
  }

298
 foreach my $key (keys %{$registry_register{$class->get_alias($db->species())}{lc($db->group())}{'_special'}}){
299
   $ret{$key} = $registry_register{$class->get_alias($db->species())}{lc($db->group())}{'_special'}{$key};
Ian Longden's avatar
Ian Longden committed
300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317
 }

  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
318 319
  caller     : internal
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
320 321 322 323 324 325

=cut

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

326 327 328 329 330
  if(!($class->alias_exists($species))){
    $class->add_alias($species,$species);
  }
  

Ian Longden's avatar
Ian Longden committed
331 332
  $species = $class->get_alias($species);

333
  $registry_register{$species}{lc($group)}{'_DB'} = $adap;
Ian Longden's avatar
Ian Longden committed
334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354

  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
355
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
356 357 358 359 360 361 362 363

=cut

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

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

364 365
  return  $registry_register{$species}{lc($group)}{'_DB'};

Ian Longden's avatar
Ian Longden committed
366 367 368 369
}

=head2 get_all_DBAdaptors

370 371 372 373 374 375 376 377
  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
378
  Status       : Stable
Ian Longden's avatar
Ian Longden committed
379 380 381 382

=cut

sub get_all_DBAdaptors{
383 384
  my ($class,@args)=@_;
  my @ret;
Ian Longden's avatar
Ian Longden committed
385

386 387 388 389 390 391 392 393 394 395 396 397 398 399 400
  my ($species, $group) = 
    rearrange([qw(SPECIES GROUP)], @args);
  if(defined($species)){
    $species = $class->get_alias($species);
  }
  foreach my $dba (@{$registry_register{'_DBA'}}){
    if(!defined($species) || $species eq $dba->species){
      if(!defined($group) || lc($group) eq lc($dba->group)){
	push @ret, $dba;
      }
    }
  }


  return \@ret;
Ian Longden's avatar
Ian Longden committed
401 402
}

403 404 405 406 407 408
=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);
409
  Status     : Stable
410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426

=cut

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

  foreach my $dba ( @{$registry_register{'_DBA'}}){
    my $dbc = $dba->dbc;
    if($dbc->equals($dbc_orig)){
      push @return, $dba;
    }
  }
  return \@return;
}


Ian Longden's avatar
Ian Longden committed
427 428 429 430 431 432 433 434 435 436 437 438
#
# 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.
  Arg [3]    : The adaptor to be added to the registry as a DNA adaptor.
  Example    : Bio::EnsEMBL::Registry->add_DNAAdaptor("Human", "core", $dnaAdap);
  Returntype : none
  Exceptions : none
439
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
440 441 442 443

=cut

sub add_DNAAdaptor{
Ian Longden's avatar
Ian Longden committed
444
  my ($class, $species, $group, $dnadb_species, $dnadb_group) = @_;
Ian Longden's avatar
Ian Longden committed
445 446

  $species = $class->get_alias($species);
447
  $dnadb_species = $class->get_alias($dnadb_species);
448
  if($dnadb_group->isa('Bio::EnsEMBL::DBSQL::DBAdaptor')){
Ian Longden's avatar
Ian Longden committed
449
    deprecated("");
450 451
  }
  else{
452 453
    $registry_register{$species}{lc($group)}{'_DNA'} = $dnadb_group;
    $registry_register{$species}{lc($group)}{'_DNA2'} = $dnadb_species;
454
  }
Ian Longden's avatar
Ian Longden committed
455 456 457 458 459 460 461 462 463
}

=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
464
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
465 466 467 468 469 470 471

=cut

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

  $species = $class->get_alias($species);
472 473
  my $new_group = $registry_register{$species}{lc($group)}{'_DNA'};
  my $new_species = $registry_register{$species}{lc($group)}{'_DNA2'};
474
  if( defined $new_group ) {
Ian Longden's avatar
Ian Longden committed
475
    return  $class->get_DBAdaptor($new_species,$new_group);
476 477 478
  } else {
    return undef;
  }
Ian Longden's avatar
Ian Longden committed
479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494
}

#
# 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
495 496
  Caller     : internal
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514


=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
#

  if(defined($reset)){ # JUST REST THE HASH VLAUE NO MORE PROCESSING NEEDED
515
    $registry_register{$species}{lc($group)}{lc($type)} = $adap;
Ian Longden's avatar
Ian Longden committed
516 517
    return;
  }
518
  if(defined($registry_register{$species}{lc($group)}{lc($type)})){ 
Ian Longden's avatar
Ian Longden committed
519
    print STDERR ("Overwriting Adaptor in Registry for $species $group $type\n");
520
    $registry_register{$species}{lc($group)}{lc($type)} = $adap;
Ian Longden's avatar
Ian Longden committed
521 522
   return;
  }
523
  $registry_register{$species}{lc($group)}{lc($type)} = $adap;
Ian Longden's avatar
Ian Longden committed
524 525 526

  if(!defined ($registry_register{$species}{'list'})){
    my @list =();
527
    push(@list,$type);
Ian Longden's avatar
Ian Longden committed
528 529 530
    $registry_register{$species}{'list'}= \@list;
  }
  else{
531
    push(@{$registry_register{$species}{'list'}},$type);
Ian Longden's avatar
Ian Longden committed
532 533
  }

534

Ian Longden's avatar
Ian Longden committed
535

536
  if(!defined ($registry_register{lc($type)}{$species})){
Ian Longden's avatar
Ian Longden committed
537 538
    my @list =();
    push(@list,$adap);
539
    $registry_register{lc($type)}{$species}= \@list;
Ian Longden's avatar
Ian Longden committed
540 541
  }
  else{
542
    push(@{$registry_register{lc($type)}{$species}},$adap);
Ian Longden's avatar
Ian Longden committed
543 544 545 546 547 548 549 550 551 552 553 554 555
  }

}


=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
556
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
557 558 559 560 561 562

=cut

sub get_adaptor{
  my ($class,$species,$group,$type)= @_;
 
563
  $species = $class->get_alias($species);
564
  my %dnadb_adaptors = qw(sequence  1 assemblymapper 1  karyotypeband 1 repeatfeature 1 coordsystem 1  assemblyexceptionfeature 1 );
565

566
  my $dnadb_group =  $registry_register{$species}{lc($group)}{_DNA};
567

568 569
  if( defined($dnadb_group) && defined($dnadb_adaptors{lc($type)}) ) {
      $species = $registry_register{$species}{lc($group)}{'_DNA2'};
570
      $group = $dnadb_group;
Ian Longden's avatar
Ian Longden committed
571 572
  }

573
  my $ret = $registry_register{$species}{lc($group)}{lc($type)};
Ian Longden's avatar
Ian Longden committed
574
  if(!defined($ret)){
575
    return undef;
Ian Longden's avatar
Ian Longden committed
576 577
  }
  if(!ref($ret)){ # not instantiated yet
578
    my $dba = $registry_register{$species}{lc($group)}{'_DB'};
Ian Longden's avatar
Ian Longden committed
579 580 581 582 583 584 585
    my $module = $ret;
    eval "require $module";

    if($@) {
      warning("$module cannot be found.\nException $@\n");
      return undef;
    }
586 587 588 589
    if(!defined($registry_register{$species}{lc($group)}{'CHECKED'})){
      $registry_register{$species}{lc($group)}{'CHECKED'} = 1;
      $class->version_check($dba);
    }
Ian Longden's avatar
Ian Longden committed
590 591 592 593 594 595 596 597 598 599
    my $adap = "$module"->new($dba);
    Bio::EnsEMBL::Registry->add_adaptor($species, $group, $type, $adap, "reset");
    $ret = $adap;
  }

  return $ret;
}

=head2 get_all_adaptors

600 601 602 603 604 605
  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
606
  Example    : @adaps = @{Bio::EnsEMBL::Registry->get_all_adaptors()};
607
  Returntype : ref to list of adaptors
Ian Longden's avatar
Ian Longden committed
608
  Exceptions : none
609
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
610 611 612 613

=cut

sub get_all_adaptors{
614 615 616 617
  my ($class,@args)= @_;
  my ($species, $group, $type);
  my @ret=();
  my (%species_hash, %group_hash, %type_hash);
Ian Longden's avatar
Ian Longden committed
618

619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651

  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'}}){ 
652
	foreach my $ty (@{$registry_register{lc($dba->species)}{'list'}}){
653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669
	  $type_hash{lc($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
670 671 672 673 674 675 676 677 678 679 680
}


=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
681
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
682 683 684 685 686 687

=cut

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

688
  $registry_register{'_ALIAS'}{lc($key)} = lc($species);
Ian Longden's avatar
Ian Longden committed
689 690 691 692 693 694 695 696
}

=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
697
  Exceptions : none
698
  Status     : Stable
Ian Longden's avatar
Ian Longden committed
699 700 701 702

=cut

sub get_alias{
703
  my ($class, $key) = @_;
Ian Longden's avatar
Ian Longden committed
704

705
  if(!defined($registry_register{'_ALIAS'}{lc($key)})){
706
    return $key;
Ian Longden's avatar
Ian Longden committed
707
  }
708
  return $registry_register{'_ALIAS'}{lc($key)};
Ian Longden's avatar
Ian Longden committed
709
}
710 711 712 713 714

=head2 alias_exists

  Arg [1]    : name of the possible alias to get species for
  Arg [2]    : if set will not throw if not found.
Ian Longden's avatar
Ian Longden committed
715
  Example    : Bio::EnsEMBL::Registry->alias_exists("Human");
716 717 718
  Description: does the species name exist.
  Returntype : 1 if exists else 0
  Exceptions : none
719
  Status     : Stable
720 721 722 723 724 725

=cut

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

726
  if(defined($registry_register{'_ALIAS'}{lc($key)})){
727 728 729 730
    return 1;
  }
  return 0;
}
731

732 733 734 735 736 737 738
=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
739
  Status     : Stable
740 741 742

=cut

743
sub set_disconnect_when_inactive{
744
  foreach my $dba ( @{get_all_DBAdaptors()}){
745 746
    my $dbc = $dba->dbc;
    #disconnect if connected
747
    $dbc->disconnect_if_idle() if $dbc->connected();
748 749 750
    $dbc->disconnect_when_inactive(1);
  }
}
Ian Longden's avatar
Ian Longden committed
751

752 753 754 755 756 757 758

=head2 disconnect_all

  Example    : Bio::EnsEMBL::Registry->disconnect_all();
  Description: disconnect from all the databases.
  Returntype : none
  Exceptions : none
759
  Status     : Stable
760 761 762

=cut

763
sub disconnect_all {
Web Admin's avatar
fixed  
Web Admin committed
764
  foreach my $dba ( @{get_all_DBAdaptors()||[]} ){
765
    my $dbc = $dba->dbc;
Web Admin's avatar
Web Admin committed
766
    next unless $dbc;
767 768 769 770
    #disconnect if connected
    $dbc->disconnect_if_idle() if $dbc->connected();
  }
}
771

772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789
=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
790
  Status     : Stable
791 792 793 794

=cut

sub change_access{
Steve Trevanion's avatar
Steve Trevanion committed
795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810
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);
	}
811 812 813
    }
}

814 815


816
=head2 load_registry_from_db
817

818 819 820 821 822 823 824 825 826 827 828 829 830 831
  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 

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

832
  Description: Will load the correct versions of the ensembl databases for the
833
               software release it can find on a database instance into the 
834
               registry. Also adds a set of standard aliases.
835 836

  Exceptions : None.
837
  Status     : Stable
838 839
 
=cut
840

841 842 843 844 845 846 847 848 849 850 851
sub load_registry_from_db{
  my($self, @args) = @_;
  my ($host, $port, $user, $pass, $verbose) =
    rearrange([qw(HOST PORT USER PASS VERBOSE)], @args);



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

  $user ||= "ensro";
852
  $port ||= 3306;
853 854 855 856 857 858
  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;
859
  my $software_version = $self->software_version();
860
  print "Will only load $software_version databases\n" if ($verbose);
861 862
  for my $db (@dbnames){
    if($db =~ /^([a-z]+_[a-z]+_[a-z]+)_(\d+)_(\d+[a-z]*)/){
863
      if($2 eq $software_version){
864 865 866 867
	$temp{$1} = $2."_".$3;
      }
    }
    elsif($db =~ /^ensembl_compara_(\d+)/){
868
      if($1 eq $software_version){
869 870 871 872
	$compara_version = $1;
      }
    }
    elsif($db =~ /^ensembl_go_(\d+)/){
873
      if($1 eq $software_version){
874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902
	$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);
  }
903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920

  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);
  }
921
  
922
  my @est_dbs = grep { /^[a-z]+_[a-z]+_est_\d+_/ } @dbnames;
923
  
924 925
  for my $est_db ( @est_dbs ) {
    my ($species, $num) = ( $est_db =~ /(^[a-z]+_[a-z]+)_est_(\d+)/ );
926
    my $dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new
927
      ( -group => "est",
928 929 930 931 932
	-species => $species,
	-host => $host,
	-user => $user,
	-pass => $pass,
	-port => $port,
933
	-dbname => $est_db
934
      );
935
    print $est_db." loaded\n" if ($verbose);
936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990
  }
  
  
  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 = Bio::EnsEMBL::Variation::DBSQL::DBAdaptor->new
	( -group => "variation",
	  -species => $species,
	  -host => $host,
	  -user => $user,
	  -pass => $pass,
	  -port => $port,
	  -dbname => $variation_db
	);
      print $variation_db." loaded\n" if ($verbose);
    }
  }
  
  #Compara
  if($compara_version){
    eval "require Bio::EnsEMBL::Compara::DBSQL::DBAdaptor";
    if($@) {
      #ignore compara as code required not there for this
      print "Bio::EnsEMBL::Compara::DBSQL::DBAdaptor not found so compara database ensembl_compara_$compara_version will be ignored\n" if ($verbose);
    }
    else{
      my $compara_db = "ensembl_compara_".$compara_version;

      my $dba = Bio::EnsEMBL::Compara::DBSQL::DBAdaptor->new
	( -group => "compara",
	  -species => "multi",
	  -host => $host,
	  -user => $user,
	  -pass => $pass,
	  -port => $port,
	  -dbname => $compara_db
	);
      print $compara_db." loaded\n" if ($verbose);       
    }
  }
  else{
    print "No Compara database found" if ($verbose);
  }


  #GO
  if($go_version){
991
    eval "require Bio::EnsEMBL::ExternalData::GO::GOAdaptor";
992 993
    if($@) {
      #ignore go as code required not there for this
994 995
#      print $@;
      print "GO software not installed so go database ensemb_go_$go_version will be ignored\n" if ($verbose);
996 997 998 999 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010 1011 1012 1013
    }
    else{
      my $go_db = "ensembl_go_".$go_version;
      my $dba = Bio::EnsEMBL::ExternalData::GO::GOAdaptor->new
	( -group => "go",
	  -species => "multi",
	  -host => $host,
	  -user => $user,
	  -pass => $pass,
	  -port => $port,
	  -dbname => $go_db
	);
      print $go_db." loaded\n" if ($verbose);              
    }
  }
  else{
    print "No go database found" if ($verbose);
  }
1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 1075 1076 1077 1078 1079 1080 1081 1082 1083 1084 1085 1086 1087

  #hard coded aliases for the different species

  my @aliases = ('chimp','PanTro1', 'Pan', 'P_troglodytes');
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Pan_troglodytes",
						 -alias => \@aliases);
  
  @aliases = ('elegans');
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Caenorhabditis_elegans", 
						 -alias => \@aliases);
  
  @aliases = ('tetraodon');
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Tetraodon_nigroviridis",
						 -alias => \@aliases);
  
  @aliases = ('H_Sapiens', 'homo sapiens', 'Homo_Sapiens', 'Homo', 'human', 'Hg17','ensHS', '9606');
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Homo_sapiens",
						 -alias => \@aliases);
  
  @aliases = ('M_Musculus', 'mus musculus', 'Mus_Musculus', 'Mus', 'mouse','Mm5','ensMM','10090');
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Mus_musculus",
						 -alias => \@aliases);
  
  @aliases = ('R_Norvegicus', 'rattus norvegicus', 'Rattus_Norvegicus', 'Rattus', 'rat', 'Rn3', '10116');
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Rattus_norvegicus",
                                               -alias => \@aliases);
  
  @aliases = ('F_Rubripes', 'fugu rubripes', 'Fugu_Rubripes', 'Fugu');
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Fugu_rubripes",
						 -alias => \@aliases);
  
  @aliases = ('G_Gallus', 'gallus gallus', 'Gallus_gallus', 'Chicken', 'GalGal2');
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Gallus_Gallus",
						 -alias => \@aliases);
  
  @aliases = ('D_Rerio', 'danio rerio', 'Danio_Rerio', 'Danio', 'zebrafish', 'zfish');
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Danio_rerio",
						 -alias => \@aliases);
  
  @aliases = ('X_Tropicalis', 'xenopus tropicalis','Xenopus_tropicalis', 'Xenopus');
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Xenopus_tropicalis",
						 -alias => \@aliases);
  
  @aliases = ('A_Gambiae', 'Anopheles Gambiae','Anopheles_gambiae', 'Anopheles','mosquito');
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Anopheles_gambiae",
						 -alias => \@aliases);
  
  @aliases = ('A_Mellifera', 'Apis Mellifera','Apis_mellifera', 'Apis', 'honeybee');
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Apis_mellifera",
						 -alias => \@aliases);
  
  @aliases = ('D_Melanogaster', 'drosophila melanogaster', 'Drosophila_melanogaster', 'drosophila', 'fly');
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Drosophila_melanogaster",
						 -alias => \@aliases);
  
  @aliases = ('S_Cerevisiae', 'Saccharomyces Cerevisiae', 
	      'Saccharomyces_cerevisiae', 'Saccharomyces', 'yeast');
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Saccharomyces_cerevisiae",
						 -alias => \@aliases);

  @aliases = ('C_Familiaris', 'Canis Familiaris', 
	      'Canis_familiaris', 'Canis', 'dog');
  
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Canis_familiaris",
						 -alias => \@aliases);
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Ciona_intestinalis",
						 -alias => ['ciona']);
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "Bos_taurus",
						 -alias => ['cow']);
  @aliases = ('compara');
  
  Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(-species => "multi",
						 -alias => \@aliases);

1088 1089
  
}
1090 1091


Ian Longden's avatar
Ian Longden committed
1092 1093 1094 1095 1096
#
# Web specific routines
#


1097

1098
=head2 DEPRECATED load_registry_with_web_adaptors
Ian Longden's avatar
Ian Longden committed
1099

1100
  DEPRECATED: Use load_registry_from_db instead.
Ian Longden's avatar
Ian Longden committed
1101 1102 1103

=cut

1104
sub load_registry_with_web_adaptors{
Ian Longden's avatar
Ian Longden committed
1105 1106
  my $class = shift;

1107
  deprecate('Use the load_registry_from_db instead'); 
Ian Longden's avatar
Ian Longden committed
1108 1109 1110 1111 1112 1113 1114
  eval{ require SiteDefs };
  if ($@){ die "Can't use SiteDefs.pm - $@\n"; }
    SiteDefs->import(qw(:ALL));

  eval{ require SpeciesDefs };
  if ($@){ die "Can't use SpeciesDefs.pm - $@\n"; }
  my $conf = new SpeciesDefs();
1115 1116 1117 1118 1119 1120
  
  my %species_alias = %{$SiteDefs::ENSEMBL_SPECIES_ALIASES};

  foreach my $spec (keys %species_alias){
    Bio::EnsEMBL::Registry->add_alias($species_alias{$spec},$spec);
  }
Ian Longden's avatar
Ian Longden committed
1121 1122 1123 1124

}

=head2 set_default_track
1125

Ian Longden's avatar
Ian Longden committed
1126 1127 1128 1129 1130 1131 1132 1133
  Sets a flag to say that that this species/group are a default track and do not
  need to be added as another web track.

  Arg [1]    : name of the species to get the adaptors for in the registry.
  Arg [2]    : name of the type to get the adaptors for in the registry.
  Example    : $merged = Bio::EnsEMBL::Registry->set_default_track("Human","core");
  Returntype : none
  Exceptions : none
1134
  Status     : At Risk.
Ian Longden's avatar
Ian Longden committed
1135 1136 1137 1138 1139 1140

=cut

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

1141 1142
  $species = get_alias($species);
  $registry_register{'def_track'}{$species}{lc($group)} = 1;
Ian Longden's avatar
Ian Longden committed
1143 1144 1145
}

=head2 default_track
1146

Ian Longden's avatar
Ian Longden committed
1147 1148 1149 1150 1151 1152 1153
  Check flag to see if this is a default track

  Arg [1]    : name of the species to get the adaptors for in the registry.
  Arg [2]    : name of the type to get the adaptors for in the registry.
  Example    : $merged = Bio::EnsEMBL::Registry->set_default_track("Human","core");
  Returntype : int 
  Exceptions : none
1154
  Status     : At Risk.
Ian Longden's avatar
Ian Longden committed
1155 1156 1157 1158 1159 1160

=cut

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

1161 1162
  $species = get_alias($species);
  if(defined($registry_register{'def_track'}{$species}{lc($group)})){
Ian Longden's avatar
Ian Longden committed
1163 1164 1165 1166 1167 1168 1169 1170
    return 1;
  }
  
  return 0;
}


=head2 add_new_tracks
1171

Ian Longden's avatar
Ian Longden committed
1172 1173 1174 1175 1176 1177 1178
  Will add new gene tracks to the configuration of the WEB server if they are
  not of the type default and the configuration already has genes in the display.

  Arg [1]    : hash of the default configuration of the web page
  Returntype : none
  Exceptions : none
  Called by  : UserConfig.pm
1179
  Status     : At Risk.
Ian Longden's avatar
Ian Longden committed
1180 1181 1182 1183
  
=cut

sub add_new_tracks{
Ian Longden's avatar
Ian Longden committed
1184
  my($class, $conf, $pos) = @_;
Ian Longden's avatar
Ian Longden committed
1185 1186 1187 1188

  my $start = 0;
  my $reg = $class;
  my $species_reg = $reg->get_alias($conf->{'species'},"nothrow");
Ian Longden's avatar
Ian Longden committed
1189
  my %pars;
Ian Longden's avatar
Ian Longden committed