comparison variant_effect_predictor/Bio/EnsEMBL/Utils/ConfigRegistry.pm @ 0:1f6dce3d34e0

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author mahtabm
date Thu, 11 Apr 2013 02:01:53 -0400
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1 =head1 LICENSE
2
3 Copyright (c) 1999-2012 The European Bioinformatics Institute and
4 Genome Research Limited. All rights reserved.
5
6 This software is distributed under a modified Apache license.
7 For license details, please see
8
9 http://www.ensembl.org/info/about/code_licence.html
10
11 =head1 CONTACT
12
13 Please email comments or questions to the public Ensembl
14 developers list at <dev@ensembl.org>.
15
16 Questions may also be sent to the Ensembl help desk at
17 <helpdesk@ensembl.org>.
18
19 =cut
20
21 =head1 NAME
22
23 Bio::EnsEMBL::Utils::ConfigRegistry;
24
25 =head1 SYNOPSIS
26
27
28 Bio::EnsEMBL::Utils::ConfigRegistry->load_core($dba);
29
30
31 =head1 DESCRIPTION
32
33 The ConfigRegistry will "Register" a set of adaptors based on the type
34 of database that is being loaded.
35
36 =head1 METHODS
37
38 =cut
39
40 package Bio::EnsEMBL::Utils::ConfigRegistry;
41
42 use strict;
43 use warnings;
44
45 use Bio::EnsEMBL::Registry;
46 my $reg = "Bio::EnsEMBL::Registry";
47 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
48 use Bio::EnsEMBL::DBSQL::DBConnection;
49 use Bio::EnsEMBL::DBSQL::DBAdaptor;
50
51 use Bio::EnsEMBL::Utils::Exception qw(warning throw deprecate stack_trace_dump);
52
53
54
55 sub gen_load {
56 my ($dba) = @_;
57 my $config_sub;
58
59 # At some point we hope to set the group in the DBadaptor, hence this
60 # long check etc. should be simpler.
61
62 if ( $dba->isa('Bio::EnsEMBL::Compara::DBSQL::DBAdaptor') ) {
63 if ( !defined( $dba->group() ) ) {
64 $dba->group('compara');
65 }
66 $config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_compara;
67 } elsif ( $dba->isa('Bio::EnsEMBL::Lite::DBAdaptor') ) {
68 if ( !defined( $dba->group() ) ) {
69 $dba->group('lite');
70 }
71 $config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_lite;
72 } elsif ( $dba->isa('Bio::EnsEMBL::External::BlastAdaptor') ) {
73 if ( !defined( $dba->group() ) ) {
74 $dba->group('blast');
75 }
76 $config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_blast;
77 } elsif ( $dba->isa('Bio::EnsEMBL::ExternalData::SNPSQL::DBAdaptor') )
78 {
79 if ( !defined( $dba->group() ) ) {
80 $dba->group('SNP');
81 }
82 $config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_SNP;
83 } elsif ( $dba->isa('Bio::EnsEMBL::Pipeline::DBSQL::DBAdaptor') ) {
84 if ( !defined( $dba->group() ) ) {
85 $dba->group('pipeline');
86 }
87 $config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_pipeline;
88 } elsif ( $dba->isa('Bio::EnsEMBL::Hive::DBSQL::DBAdaptor') ) {
89 if ( !defined( $dba->group() ) ) {
90 $dba->group('hive');
91 }
92 $config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_hive;
93 } elsif (
94 $dba->isa('Bio::EnsEMBL::ExternalData::Haplotype::DBAdaptor') )
95 {
96 if ( !defined( $dba->group() ) ) {
97 $dba->group('haplotype');
98 }
99 $config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_haplotype;
100 } elsif ( $dba->isa('Bio::EnsEMBL::Variation::DBSQL::DBAdaptor') ) {
101 if ( !defined( $dba->group() ) ) {
102 $dba->group('variation');
103 }
104 $config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_variation;
105 } elsif ( $dba->isa('Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor') ) {
106 if ( !defined( $dba->group() ) ) {
107 $dba->group('funcgen');
108 }
109 $config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_funcgen;
110 } elsif ( $dba->isa('Bio::Ensembl::DBSQL::OntologyTermAdaptor') ) {
111 if ( !defined( $dba->group() ) ) {
112 $dba->group('ontology');
113 }
114 $config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_ontology;
115 } elsif ( $dba->isa('Bio::EnsEMBL::DBSQL::DBAdaptor') ) {
116 #vega uses the core DBAdaptor so test if vega is in the dbname
117 if ( !defined( $dba->group() ) ) {
118 $dba->group('core');
119 }
120
121 if ( $dba->group eq "estgene" ) {
122 $config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_estgene;
123 } elsif ( $dba->group eq "otherfeatures" ) {
124 $config_sub =
125 \&Bio::EnsEMBL::Utils::ConfigRegistry::load_otherfeatures;
126 } elsif ( $dba->group eq 'vega' || $dba->group eq 'vega_update' ) {
127 $config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_vega;
128 } else {
129 $config_sub = \&Bio::EnsEMBL::Utils::ConfigRegistry::load_core;
130 }
131
132 } else {
133 # none standard DBA adaptor
134 if ( !defined( $dba->group() ) ) {
135 $dba->group('none_standard');
136 }
137 $config_sub =
138 \&Bio::EnsEMBL::Utils::ConfigRegistry::load_and_attach_dnadb_to_core;
139 # throw("Unknown DBAdaptor type $dba\n");
140 }
141
142 # return if the connection and species, group are the same
143
144 if ( defined( $dba->species ) ) {
145 my $db_reg = $reg->get_DBAdaptor( $dba->species, $dba->group, 1 );
146 if ( defined($db_reg) ) {
147 if ( $dba->dbc->equals( $db_reg->dbc ) ) { return $db_reg }
148 else {
149 my $msg =
150 sprintf( 'WARN: Species (%s) and group (%s) '
151 . 'same for two seperate databases',
152 $dba->species(), $dba->group() );
153
154 warn "${msg}\nModify species name for one of these\n";
155 $dba->species(
156 find_unique_species( $dba->species, $dba->group ) );
157 }
158 }
159 } else { # no species
160
161 my @db_reg =
162 @{ $reg->get_all_DBAdaptors_by_connection( $dba->dbc ) };
163
164 foreach my $db_adaptor (@db_reg) {
165 if ( $db_adaptor->group eq $dba->group ) {
166 # found same db connection and group
167 return $db_adaptor;
168 }
169 }
170
171 $dba->species( find_unique_species( "DEFAULT", $dba->group ) );
172 if ( $dba->species ne "DEFAULT" ) {
173 warn "WARN: For multiple species "
174 . "use species attribute in DBAdaptor->new()\n";
175 }
176 }
177
178 Bio::EnsEMBL::Registry->add_DBAdaptor( $dba->species(), $dba->group(),
179 $dba );
180
181 #call the loading subroutine. (add the adaptors to the DBAdaptor)
182 &{$config_sub}($dba);
183
184 return $dba;
185 } ## end sub gen_load
186
187
188
189 sub find_unique_species {
190 my ( $species, $group ) = @_;
191
192 $reg->add_alias( $species, $species );
193
194 my $i = 0;
195 my $free = 0;
196
197 while ( !$free ) {
198 if ( $i == 0 ) {
199 if ( !defined( $reg->get_DBAdaptor( $species, $group ) ) ) {
200 $free = 1;
201 $i = "";
202 } else {
203 $i = 1;
204 }
205 } else {
206 # set needed self alias
207 $reg->add_alias( $species . $i, $species . $i );
208
209 if ( !defined( $reg->get_DBAdaptor( $species . $i, $group ) ) ) {
210 $free = 1;
211 } else {
212 $i++;
213 }
214 }
215 }
216
217 $species .= $i;
218 return ($species);
219 } ## end sub find_unique_species
220
221
222
223 sub load_adaptors {
224 my ($dba) = @_;
225
226 my %pairs = %{ $dba->get_available_adaptors() };
227
228 while ( my ( $key, $value ) = each(%pairs) ) {
229 Bio::EnsEMBL::Registry->add_adaptor( $dba->species(), $dba->group(),
230 $key, $value );
231 }
232 }
233
234 sub load_and_attach_dnadb_to_core {
235 my ($dba) = @_;
236
237 load_adaptors($dba);
238 $reg->add_DNAAdaptor( $dba->species(), $dba->group(), $dba->species(),
239 'core' );
240 }
241
242
243 =head2 load_core
244 Arg [1] : DBAdaptor with DBConnection already attached
245 Returntype : DBAdaptor
246 Exceptions : none
247 =cut
248 sub load_core { load_adaptors(@_) }
249
250
251 #
252 # 1) core. no need to add dnadb
253 # 2) not core add dnadb
254 # 3)
255 #
256
257 =head2 load_compara
258 Arg [1] : DBAdaptor with DBConnection already attached
259 Returntype : DBAdaptor
260 Exceptions : none
261 =cut
262 sub load_compara { load_adaptors(@_) }
263
264 =head2 load_hive
265 Arg [1] : DBAdaptor with DBConnection already attached
266 Returntype : DBAdaptor
267 Exceptions : none
268 =cut
269 sub load_hive { load_adaptors(@_) }
270
271 =head2 load_pipeline
272 Arg [1] : DBAdaptor with DBConnection already attached
273 Returntype : DBAdaptor
274 Exceptions : none
275 =cut
276 sub load_pipeline { load_adaptors(@_) }
277
278 =head2 load_SNP
279 Arg [1] : DBAdaptor with DBConnection already attached
280 Returntype : DBAdaptor
281 Exceptions : none
282 =cut
283 sub load_SNP { load_adaptors(@_) }
284
285 sub load_haplotype { load_adaptors(@_) }
286
287 sub load_ontology { load_adaptors(@_) }
288
289
290 # these that need to attach to the core to get the sequence data
291
292 sub load_estgene { load_and_attach_dnadb_to_core(@_) }
293
294 sub load_variation { load_and_attach_dnadb_to_core(@_) }
295
296 sub load_funcgen { load_and_attach_dnadb_to_core(@_) }
297
298 =head2 load_otherfeatures
299 Arg [1] : DBAdaptor with DBConnection alredy attached
300 Returntype : DBAdaptor
301 Exceptions : none
302
303 =cut
304 sub load_otherfeatures { load_and_attach_dnadb_to_core(@_) }
305
306 =head2 load_vega
307 Arg [1] : DBAdaptor with DBConnection already attached
308 Returntype : DBAdaptor
309 Exceptions : none
310 =cut
311 sub load_vega { load_and_attach_dnadb_to_core(@_) }
312
313
314 sub add_alias {
315 my ( $class, @args ) = @_;
316
317 my ( $species, $aliases ) = rearrange( [qw(SPECIES ALIAS)], @args );
318
319 # Make sure it exists itself
320 Bio::EnsEMBL::Registry->add_alias( $species, $species );
321
322 if ( defined($aliases) ) {
323 foreach my $ali (@$aliases) {
324 Bio::EnsEMBL::Registry->add_alias( $species, $ali );
325 }
326 }
327 }
328
329 #
330 # overwrite/load new types. Done this way to enable no changes to CVS for
331 # external users. External users should add there own "GROUPS" in the file
332 # User_defined_load.
333 #
334
335 eval{ require Bio::EnsEMBL::Utils::User_defined_load };
336
337 1;