DBAdaptor.pm 11.8 KB
Newer Older
1
=pod
2 3 4

=head1 NAME

5
    Bio::EnsEMBL::Hive::DBSQL::DBAdaptor
6 7 8

=head1 SYNOPSIS

9
    my $db = Bio::EnsEMBL::Hive::DBSQL::DBAdaptor->new( -url => 'mysql://my_username:my_password@my_hostname:3306/my_hive_database' );
10 11

=head1 DESCRIPTION
12

13 14 15 16
    This object represents the handle for a Hive system enabled database

=head1 LICENSE

17
    Copyright [1999-2014] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
18 19 20 21 22 23 24 25 26

    Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
    You may obtain a copy of the License at

         http://www.apache.org/licenses/LICENSE-2.0

    Unless required by applicable law or agreed to in writing, software distributed under the License
    is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
    See the License for the specific language governing permissions and limitations under the License.
27 28 29

=head1 CONTACT

30
    Please subscribe to the Hive mailing list:  http://listserver.ebi.ac.uk/mailman/listinfo/ehive-users  to discuss Hive-related questions or to be notified of our updates
31 32 33 34 35 36 37

=cut


package Bio::EnsEMBL::Hive::DBSQL::DBAdaptor;

use strict;
38
use warnings;
39

40
use Bio::EnsEMBL::Hive;
41
use Bio::EnsEMBL::Hive::DBSQL::DBConnection;
42
use Bio::EnsEMBL::Hive::DBSQL::SqlSchemaAdaptor;
43 44
use Bio::EnsEMBL::Hive::Utils ('throw');
use Bio::EnsEMBL::Hive::Utils::Collection;
45 46 47

use Bio::EnsEMBL::Hive::MetaParameters;
use Bio::EnsEMBL::Hive::PipelineWideParameters;
48 49 50 51
use Bio::EnsEMBL::Hive::ResourceClass;
use Bio::EnsEMBL::Hive::ResourceDescription;
use Bio::EnsEMBL::Hive::Analysis;
use Bio::EnsEMBL::Hive::AnalysisStats;
52

53

54
sub new {
55 56
    my $class = shift @_;
    my %flags = @_;
57

58 59
    my ($dbc, $url, $reg_conf, $reg_type, $reg_alias, $species, $no_sql_schema_version_check)
        = @flags{qw(-dbconn -url -reg_conf -reg_type -reg_alias -species -no_sql_schema_version_check)};
60

61 62
    $url .= ';nosqlvc=1' if($url && $no_sql_schema_version_check);

63 64 65 66 67
    if($reg_conf or $reg_alias) {   # need to initialize Registry even if $reg_conf is not really given
        require Bio::EnsEMBL::Registry;
        Bio::EnsEMBL::Registry->load_all($reg_conf);    # if undefined, default reg_conf will be used
    }

68 69 70
    my $self;

    if($url) {
71

72
        $dbc = Bio::EnsEMBL::Hive::DBSQL::DBConnection->new(-url => $url)
73 74
            or die "Unable to create a DBC using url='$url'";

75
    } elsif($reg_alias) {
76

77 78 79 80 81 82
        $reg_type ||= 'hive';

        $self = Bio::EnsEMBL::Registry->get_DBAdaptor($reg_alias, $reg_type)
            or die "Unable to connect to DBA using reg_conf='$reg_conf', reg_type='$reg_type', reg_alias='$reg_alias'\n";

        if($reg_type ne 'hive') {   # ensure we are getting a Hive adaptor even from a non-Hive Registry entry:
83
            $dbc = $self->dbc;
84
            $self = undef;
85
        }
86 87
    }

88
    if($dbc && !$self) {
89
        $self = bless {}, $class;
90
        $self->dbc( $dbc );
91
    }
92 93

    unless($no_sql_schema_version_check) {
94 95

        my $dbc = $self->dbc();
96
        my $safe_url = $dbc->url('EHIVE_PASS');
97 98

        my $code_sql_schema_version = Bio::EnsEMBL::Hive::DBSQL::SqlSchemaAdaptor->get_code_sql_schema_version()
99
            || die "DB($safe_url) Could not establish code_sql_schema_version, please check that 'EHIVE_ROOT_DIR' environment variable is set correctly";
100

101
        my $db_sql_schema_version   = eval { $self->get_MetaAdaptor->get_value_by_key( 'hive_sql_schema_version' ); };
102
        if($@) {
103
            if($@ =~ /hive_meta.*doesn't exist/) {
104

105
                die "\nDB($safe_url) The 'hive_meta' table does not seem to exist in the database yet.\nPlease patch the database up to sql_schema_version '$code_sql_schema_version' and try again.\n";
106 107 108

            } else {

109
                die "DB($safe_url) $@";
110
            }
111 112 113

        } elsif(!$db_sql_schema_version) {

114
            die "\nDB($safe_url) The 'hive_meta' table does not contain 'hive_sql_schema_version' entry.\nPlease investigate.\n";
115 116 117

        } elsif($db_sql_schema_version < $code_sql_schema_version) {

118
            my $new_patches = Bio::EnsEMBL::Hive::DBSQL::SqlSchemaAdaptor->get_sql_schema_patches( $db_sql_schema_version, $dbc->driver )
119
                || die "DB($safe_url) sql_schema_version mismatch: the database's version is '$db_sql_schema_version' but the code is already '$code_sql_schema_version'.\n"
120 121
                      ."Unfortunately we cannot patch the database; you may have to create a new database or agree to run older code\n";

122
            my $patcher_command = "$ENV{'EHIVE_ROOT_DIR'}/scripts/db_cmd.pl -url $safe_url";
123

124
            die "DB($safe_url) sql_schema_version mismatch: the database's version is '$db_sql_schema_version' but the code is already '$code_sql_schema_version'.\n"
125
               ."Please upgrade the database by applying the following patches:\n\n".join("\n", map { "\t$patcher_command < $_" } @$new_patches)."\n\nand try again.\n";
126 127 128

        } elsif($code_sql_schema_version < $db_sql_schema_version) {

129
            die "DB($safe_url) sql_schema_version mismatch: the database's version is '$db_sql_schema_version', but your code is still '$code_sql_schema_version'.\n"
130
               ."Please update the code and try again.\n";
131
        }
132
    }
133

134 135 136 137 138
    if($species) {      # [compatibility with core code] store the DBAdaptor in Registry:
        require Bio::EnsEMBL::Registry;
        Bio::EnsEMBL::Registry->add_DBAdaptor( $species, 'hive', $self );
    }

139
    return $self;
140 141 142
}


143
sub dbc {
144
    my $self = shift;
145

146
    $self->{'_dbc'} = bless shift, 'Bio::EnsEMBL::Hive::DBSQL::DBConnection' if(@_);
147

148
    return $self->{'_dbc'};
149 150 151
}


152 153 154 155
sub hive_use_triggers {  # getter only, not setter
    my $self = shift @_;

    unless( defined($self->{'_hive_use_triggers'}) ) {
156
        my $hive_use_triggers = $self->get_MetaAdaptor->get_value_by_key( 'hive_use_triggers' );
157
        $self->{'_hive_use_triggers'} = $hive_use_triggers // 0;
158 159 160 161 162
    } 
    return $self->{'_hive_use_triggers'};
}


163 164 165 166
sub hive_use_param_stack {  # getter only, not setter
    my $self = shift @_;

    unless( defined($self->{'_hive_use_param_stack'}) ) {
167
        my $hive_use_param_stack = $self->get_MetaAdaptor->get_value_by_key( 'hive_use_param_stack' );
168
        $self->{'_hive_use_param_stack'} = $hive_use_param_stack // 0;
169 170 171 172 173
    } 
    return $self->{'_hive_use_param_stack'};
}


174 175 176 177 178 179 180 181 182 183 184
sub hive_auto_rebalance_semaphores {  # getter only, not setter
    my $self = shift @_;

    unless( defined($self->{'_hive_auto_rebalance_semaphores'}) ) {
        my $hive_auto_rebalance_semaphores = $self->get_MetaAdaptor->get_value_by_key( 'hive_auto_rebalance_semaphores' );
        $self->{'_hive_auto_rebalance_semaphores'} = $hive_auto_rebalance_semaphores // 0;
    } 
    return $self->{'_hive_auto_rebalance_semaphores'};
}


185 186 187 188 189 190 191 192 193 194
our %adaptor_type_2_package_name = (
    'Accumulator'           => 'Bio::EnsEMBL::Hive::DBSQL::AccumulatorAdaptor',
    'Analysis'              => 'Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor',
    'AnalysisCtrlRule'      => 'Bio::EnsEMBL::Hive::DBSQL::AnalysisCtrlRuleAdaptor',
    'AnalysisData'          => 'Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor',
    'AnalysisJob'           => 'Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor',
    'AnalysisStats'         => 'Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor',
    'DataflowRule'          => 'Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor',
    'LogMessage'            => 'Bio::EnsEMBL::Hive::DBSQL::LogMessageAdaptor',
    'Meta'                  => 'Bio::EnsEMBL::Hive::DBSQL::MetaAdaptor',
195
    'PipelineWideParameters'=> 'Bio::EnsEMBL::Hive::DBSQL::PipelineWideParametersAdaptor',
196 197 198
    'NakedTable'            => 'Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor',
    'ResourceClass'         => 'Bio::EnsEMBL::Hive::DBSQL::ResourceClassAdaptor',
    'ResourceDescription'   => 'Bio::EnsEMBL::Hive::DBSQL::ResourceDescriptionAdaptor',
199
    'Role'                  => 'Bio::EnsEMBL::Hive::DBSQL::RoleAdaptor',
200 201 202 203 204
    'Queen'                 => 'Bio::EnsEMBL::Hive::Queen',

        # aliases:
    'Job'                   => 'Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor',
    'Worker'                => 'Bio::EnsEMBL::Hive::Queen',
205
    'MetaParameters'        => 'Bio::EnsEMBL::Hive::DBSQL::MetaAdaptor',
206 207 208
);


Leo Gordon's avatar
Leo Gordon committed
209
sub get_available_adaptors {
210 211

    return \%adaptor_type_2_package_name;
212
}
213

214

215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238
sub parse_underscored_id_name {
    my ($self, $underscored_id_name) = @_;

    my ($is_an_id, $foo_id_method_name, $foo_obj_method_name);

    my @syll = split(/_/, $underscored_id_name);
    if($syll[scalar(@syll)-1] eq 'id') {
        pop @syll;
        ($is_an_id, $foo_id_method_name, $foo_obj_method_name) = ( 1, $underscored_id_name, join('_', @syll) );
    } else {
        ($is_an_id, $foo_id_method_name, $foo_obj_method_name) = ( 0, $underscored_id_name .'_id' , $underscored_id_name );
    }

    my $AdaptorType = '';   # will be growing from right to left
    while(@syll) {
        $AdaptorType = ucfirst(pop @syll) . $AdaptorType;
        if(exists( $self->get_available_adaptors->{ $AdaptorType })) {
            return ($AdaptorType, $is_an_id, $foo_id_method_name, $foo_obj_method_name);
        }
    }
    return;   # could not parse
}


239 240
sub get_adaptor {
    my $self = shift;
241 242 243 244
    my $AdaptorType = shift;

    my $adaptor_package_name = $self->get_available_adaptors()->{$AdaptorType}
        or throw("Could not find a module corresponding to '$AdaptorType'");
245

246
    my $signature = join(':', $adaptor_package_name, @_);
247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278

    unless( $self->{'_cached_adaptor'}{$signature} ) {

        eval "require $adaptor_package_name"
        or throw("Could not load or compile module '$adaptor_package_name'");

        $self->{'_cached_adaptor'}{$signature} = $adaptor_package_name->new( $self, @_ );
    }

    return $self->{'_cached_adaptor'}{$signature};
}


sub DESTROY { }   # to simplify AUTOLOAD

sub AUTOLOAD {
    our $AUTOLOAD;

    my $type;
    if ( $AUTOLOAD =~ /^.*::get_(\w+)Adaptor$/ ) {
        $type = $1;
    } elsif ( $AUTOLOAD =~ /^.*::get_(\w+)$/ ) {
        $type = $1;
    } else {
        die "DBAdaptor::AUTOLOAD: Could not interpret the method: $AUTOLOAD";
    }

    my $self = shift;

    return $self->get_adaptor($type, @_);
}

279

280 281
sub init_collections {  # should not really belong to DBAdaptor, temporarily squatting here...

282
    foreach my $AdaptorType ('MetaParameters', 'PipelineWideParameters', 'ResourceClass', 'ResourceDescription', 'Analysis', 'AnalysisStats', 'AnalysisCtrlRule', 'DataflowRule') {
283 284 285 286 287 288
        my $class = 'Bio::EnsEMBL::Hive::'.$AdaptorType;
        $class->collection( Bio::EnsEMBL::Hive::Utils::Collection->new() );
    }
}


289 290 291
sub load_collections {
    my $self = shift @_;

292
    foreach my $AdaptorType ('MetaParameters', 'PipelineWideParameters', 'ResourceClass', 'ResourceDescription', 'Analysis', 'AnalysisStats', 'AnalysisCtrlRule', 'DataflowRule') {
293
        my $adaptor = $self->get_adaptor( $AdaptorType );
294 295
        my $class = 'Bio::EnsEMBL::Hive::'.$AdaptorType;
        $class->collection( Bio::EnsEMBL::Hive::Utils::Collection->new( $adaptor->fetch_all ) );
296 297 298 299 300 301 302
    }
}


sub save_collections {
    my $self = shift @_;

303
    foreach my $AdaptorType ('MetaParameters', 'PipelineWideParameters', 'ResourceClass', 'ResourceDescription', 'Analysis', 'AnalysisStats', 'AnalysisCtrlRule', 'DataflowRule') {
304
        my $adaptor = $self->get_adaptor( $AdaptorType );
305 306
        my $class = 'Bio::EnsEMBL::Hive::'.$AdaptorType;
        foreach my $storable_object ( $class->collection()->list ) {
307
            $adaptor->store_or_update_one( $storable_object, $class->unikey() );
308 309 310 311 312
#            warn "Stored/updated ".$storable_object->toString()."\n";
        }
    }

    my $job_adaptor = $self->get_AnalysisJobAdaptor;
313
    foreach my $analysis ( Bio::EnsEMBL::Hive::Analysis->collection()->list ) {
314 315 316 317 318 319 320 321 322
        if(my $our_jobs = $analysis->jobs_collection ) {
            $job_adaptor->store( $our_jobs );
            foreach my $job (@$our_jobs) {
#                warn "Stored ".$job->toString()."\n";
            }
        }
    }
}

323
1;
324