BaseAdaptor.pm 19.5 KB
Newer Older
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
=pod 

=head1 NAME

    Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor

=head1 DESCRIPTION

    The base class for all other Object- or NakedTable- adaptors.
    Performs the low-level SQL needed to retrieve and store data in tables.

=head1 EXTERNAL DEPENDENCIES

    DBI 1.6

=head1 LICENSE

18
    Copyright [1999-2014] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
19
20
21
22
23
24
25
26
27
28
29
30

    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.

=head1 CONTACT

31
    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
32
33
34
35

=cut


36
37
38
package Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor;

use strict;
39
use warnings;
40
no strict 'refs';   # needed to allow AUTOLOAD create new methods
41
use DBI 1.6;        # the 1.6 functionality is important for detecting autoincrement fields and other magic.
42

43
use Bio::EnsEMBL::Hive::Utils ('stringify', 'throw');
44

45
46
47
48
49
50
51
52
53
54
55

sub default_table_name {
    die "Please define table_name either by setting it via table_name() method or by redefining default_table_name() in your adaptor class";
}


sub default_insertion_method {
    return 'INSERT_IGNORE';
}


56
57
58
59
sub default_overflow_limit {
    return {
        # 'overflow_column1_name' => column1_size,
        # 'overflow_column2_name' => column2_size,
60
61
62
63
64
65
66
67
68
        # ...
    };
}

sub default_input_column_mapping {
    return {
        # 'original_column1' => "original_column1*10 AS c1_times_ten",
        # 'original_column2' => "original_column2+1 AS c2_plus_one",
        # ...
69
70
71
    };
}

72
73
74
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
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
# ---------------------------------------------------------------------------

sub new {
    my ( $class, $dbobj ) = @_;

    my $self = bless {}, $class;

    if ( !defined $dbobj || !ref $dbobj ) {
        throw("Don't have a db [$dbobj] for new adaptor");
    }

    if ( ref($dbobj) =~ /DBConnection$/ ) {
        $self->dbc($dbobj);
    } elsif( UNIVERSAL::can($dbobj, 'dbc') ) {
        $self->dbc( $dbobj->dbc );
        $self->db( $dbobj );
    } else {
        throw("I was given [$dbobj] for a new adaptor");
    }

    return $self;
}


sub db {
    my $self = shift @_;

    if(@_) {    # setter
        $self->{_db} = shift @_;
    }
    return $self->{_db};
}


sub dbc {
    my $self = shift @_;

    if(@_) {    # setter
        $self->{_dbc} = shift @_;
    }
    return $self->{_dbc};
}


sub prepare {
    my ( $self, $sql ) = @_;

    # Uncomment next line to cancel caching on the SQL side.
    # Needed for timing comparisons etc.
    #$sql =~ s/SELECT/SELECT SQL_NO_CACHE/i;

    return $self->dbc->prepare($sql);
}

126
127
128
129
130
131
132
133
134
135
136

sub overflow_limit {
    my $self = shift @_;

    if(@_) {    # setter
        $self->{_overflow_limit} = shift @_;
    }
    return $self->{_overflow_limit} || $self->default_overflow_limit();
}


137
138
139
140
141
142
143
144
145
146
sub input_column_mapping {
    my $self = shift @_;

    if(@_) {    # setter
        $self->{_input_column_mapping} = shift @_;
    }
    return $self->{_input_column_mapping} || $self->default_input_column_mapping();
}


147
148
149
150
151
sub table_name {
    my $self = shift @_;

    if(@_) {    # setter
        $self->{_table_name} = shift @_;
152
        $self->_table_info_loader();
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
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
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
    }
    return $self->{_table_name} || $self->default_table_name();
}


sub insertion_method {
    my $self = shift @_;

    if(@_) {    # setter
        $self->{_insertion_method} = shift @_;
    }
    return $self->{_insertion_method} || $self->default_insertion_method();
}


sub column_set {
    my $self = shift @_;

    if(@_) {    # setter
        $self->{_column_set} = shift @_;
    } elsif( !defined( $self->{_column_set} ) ) {
        $self->_table_info_loader();
    }
    return $self->{_column_set};
}


sub primary_key {        # not necessarily auto-incrementing
    my $self = shift @_;

    if(@_) {    # setter
        $self->{_primary_key} = shift @_;
    } elsif( !defined( $self->{_primary_key} ) ) {
        $self->_table_info_loader();
    }
    return $self->{_primary_key};
}


sub updatable_column_list {    # it's just a cashed view, you cannot set it directly
    my $self = shift @_;

    unless($self->{_updatable_column_list}) {
        my %primary_key_set = map { $_ => 1 } @{$self->primary_key()};
        my $column_set      = $self->column_set();
        $self->{_updatable_column_list} = [ grep { not $primary_key_set{$_} } keys %$column_set ];
    }
    return $self->{_updatable_column_list};
}


sub autoinc_id {
    my $self = shift @_;

    if(@_) {    # setter
        $self->{_autoinc_id} = shift @_;
    } elsif( !defined( $self->{_autoinc_id} ) ) {
        $self->_table_info_loader();
    }
    return $self->{_autoinc_id};
}


sub _table_info_loader {
    my $self = shift @_;

    my $dbc         = $self->dbc();
220
    my $dbh         = $dbc->db_handle();
221
    my $driver      = $dbc->driver();
222
    my $dbname      = $dbc->dbname();
223
224
225
226
    my $table_name  = $self->table_name();

    my %column_set  = ();
    my $autoinc_id  = '';
227
228
229
230
231
    my @primary_key = $dbh->primary_key(undef, undef, $table_name);

    my $sth = $dbh->column_info(undef, undef, $table_name, '%');
    $sth->execute();
    while (my $row = $sth->fetchrow_hashref()) {
232
233
234
        my ( $column_name, $column_type ) = @$row{'COLUMN_NAME', 'TYPE_NAME'};

        # warn "ColumnInfo [$table_name/$column_name] = $column_type\n";
235

236
        $column_set{$column_name}  = $column_type;
237

238
        if( ($column_name eq $table_name.'_id')
239
         or ($table_name eq 'analysis_base' and $column_name eq 'analysis_id') ) {    # a special case (historical)
240
            $autoinc_id = $column_name;
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
        }
    }
    $sth->finish;

    $self->column_set(  \%column_set );
    $self->primary_key( \@primary_key );
    $self->autoinc_id(   $autoinc_id );
}


sub count_all {
    my ($self, $constraint) = @_;

    my $table_name      = $self->table_name();

    my $sql = "SELECT COUNT(*) FROM $table_name";

258
259
260
    if($constraint) {
            # in case $constraint contains any kind of JOIN (regular, LEFT, RIGHT, etc) do not put WHERE in front:
        $sql .= (($constraint=~/\bJOIN\b/i) ? ' ' : ' WHERE ') . $constraint;
261
262
    }

263
    # warn "SQL: $sql\n";
264
265
266

    my $sth = $self->prepare($sql);
    $sth->execute;  
267
    my ($count) = $sth->fetchrow_array();
268
269
270
271
272
273
274
    $sth->finish;  

    return $count;
}


sub fetch_all {
275
276
    my ($self, $constraint, $one_per_key, $key_list, $value_column) = @_;
    
277
278
    my $table_name              = $self->table_name();
    my $input_column_mapping    = $self->input_column_mapping();
279

280
    my $sql = 'SELECT ' . join(', ', map { $input_column_mapping->{$_} // "$table_name.$_" } keys %{$self->column_set()}) . " FROM $table_name";
281
282

    if($constraint) { 
283
            # in case $constraint contains any kind of JOIN (regular, LEFT, RIGHT, etc) do not put WHERE in front:
284
        $sql .= (($constraint=~/\bJOIN\b/i or $constraint=~/^LIMIT|ORDER|GROUP/) ? ' ' : ' WHERE ') . $constraint;
285
286
    }

287
    # warn "SQL: $sql\n";
288
289
290
291

    my $sth = $self->prepare($sql);
    $sth->execute;  

292
293
294
    my @overflow_columns = keys %{ $self->overflow_limit() };
    my $overflow_adaptor = scalar(@overflow_columns) && $self->db->get_AnalysisDataAdaptor();

295
    my $result_struct;  # will be autovivified to the correct data structure
296
297

    while(my $hashref = $sth->fetchrow_hashref) {
298
299
300
301
302
303
304

        foreach my $overflow_key (@overflow_columns) {
            if($hashref->{$overflow_key} =~ /^_ext(?:\w+)_data_id (\d+)$/) {
                $hashref->{$overflow_key} = $overflow_adaptor->fetch_by_analysis_data_id_TO_data($1);
            }
        }

305
        my $pptr = \$result_struct;
306
307
308
309
        if($key_list) {
            foreach my $syll (@$key_list) {
                $pptr = \$$pptr->{$hashref->{$syll}};   # using pointer-to-pointer to enforce same-level vivification
            }
310
311
312
313
314
315
        }
        my $object = $value_column
            ? $hashref->{$value_column}
            : $self->objectify($hashref);
        if($one_per_key) {
            $$pptr = $object;
316
        } else {
317
            push @$$pptr, $object;
318
319
320
321
        }
    }
    $sth->finish;  

322
    unless(defined($result_struct)) {
323
        if($key_list and scalar(@$key_list)) {
324
325
326
327
328
329
330
            $result_struct = {};
        } elsif(!$one_per_key) {
            $result_struct = [];
        }
    }

    return $result_struct;  # either listref or hashref is returned, depending on the call parameters
331
332
333
334
}


sub primary_key_constraint {
335
336
    my $self        = shift @_;
    my $sliceref    = shift @_;
337
338
339
340

    my $primary_key  = $self->primary_key();  # Attention: the order of primary_key columns of your call should match the order in the table definition!

    if(@$primary_key) {
341
        return join (' AND ', map { $primary_key->[$_]."='".$sliceref->[$_]."'" } (0..scalar(@$primary_key)-1));
342
343
344
345
346
347
348
349
350
351
    } else {
        my $table_name = $self->table_name();
        die "Table '$table_name' doesn't have a primary_key";
    }
}


sub fetch_by_dbID {
    my $self = shift @_;    # the rest in @_ should be primary_key column values

352
    return $self->fetch_all( $self->primary_key_constraint( \@_ ), 1 );
353
354
355
}


356
357
358
sub remove_all {    # remove entries by a constraint
    my $self        = shift @_;
    my $constraint  = shift @_ || 1;
359

360
    my $table_name  = $self->table_name();
361

362
    my $sql = "DELETE FROM $table_name WHERE $constraint";
363
364
365
366
367
368
    my $sth = $self->prepare($sql);
    $sth->execute();
    $sth->finish();
}


369
370
371
372
373
374
375
376
377
378
sub remove {    # remove the object by primary_key
    my $self        = shift @_;
    my $object      = shift @_;

    my $primary_key_constraint  = $self->primary_key_constraint( $self->slicer($object, $self->primary_key()) );

    return $self->remove_all( $primary_key_constraint );
}


379
380
381
382
383
384
385
386
387
388
389
390
391
sub update {    # update (some or all) non_primary columns from the primary
    my $self    = shift @_;
    my $object  = shift @_;    # the rest in @_ should be the column names to be updated

    my $table_name              = $self->table_name();
    my $primary_key_constraint  = $self->primary_key_constraint( $self->slicer($object, $self->primary_key()) );
    my $columns_to_update       = scalar(@_) ? \@_ : $self->updatable_column_list();
    my $values_to_update        = $self->slicer( $object, $columns_to_update );

    unless(@$columns_to_update) {
        die "There are no dependent columns to update, as everything seems to belong to the primary key";
    }

392
    my $sql = "UPDATE $table_name SET ".join(', ', map { "$_=?" } @$columns_to_update)." WHERE $primary_key_constraint";
393
    # warn "SQL: $sql\n";
394
    my $sth = $self->prepare($sql);
395
    # warn "VALUES_TO_UPDATE: ".join(', ', map { "'$_'" } @$values_to_update)."\n";
396
397
    $sth->execute( @$values_to_update);

398
399
400
    $sth->finish();
}

401

402
sub store_or_update_one {
403
    my ($self, $object, $filter_columns) = @_;
404

405
    #use Data::Dumper;
406
    if(UNIVERSAL::can($object, 'adaptor') and $object->adaptor and $object->adaptor==$self) {  # looks like it has been previously stored
407
        if( @{ $self->primary_key() } and @{ $self->updatable_column_list() } ) {
408
            $self->update( $object );
409
410
411
            #warn "store_or_update_one: updated [".(UNIVERSAL::can($object, 'toString') ? $object->toString : Dumper($object))."]\n";
        } else {
            #warn "store_or_update_one: non-updatable [".(UNIVERSAL::can($object, 'toString') ? $object->toString : Dumper($object))."]\n";
412
        }
413
    } elsif( my $present = $self->check_object_present_in_db_by_content( $object, $filter_columns ) ) {
414
        $self->mark_stored($object, $present);
415
416
417
418
419
        #warn "store_or_update_one: found [".(UNIVERSAL::can($object, 'toString') ? $object->toString : Dumper($object))."] in db by content of (".join(', ', @$filter_columns).")\n";
        if( @{ $self->primary_key() } and @{ $self->updatable_column_list() } ) {
            #warn "store_or_update_one: updating the columns (".join(', ', @{ $self->updatable_column_list() }).")\n";
            $self->update( $object );
        }
420
421
    } else {
        $self->store( $object );
422
        #warn "store_or_update_one: stored [".(UNIVERSAL::can($object, 'toString') ? $object->toString : Dumper($object))."]\n";
423
424
425
    }
}

426

427
428
sub check_object_present_in_db_by_content {    # return autoinc_id/undef if the table has autoinc_id or just 1/undef if not
    my ( $self, $object, $filter_columns ) = @_;
429
430
431
432
433

    my $table_name  = $self->table_name();
    my $column_set  = $self->column_set();
    my $autoinc_id  = $self->autoinc_id();

434
435
436
437
438
439
440
441
442
    if($filter_columns) {
            # make sure all fields exist in the database as columns:
        $filter_columns = [ map { $column_set->{$_} ? $_ : $_.'_id' } @$filter_columns ];
    } else {
            # we look for identical contents, so must skip the autoinc_id columns when fetching:
        $filter_columns = [ grep { $_ ne $autoinc_id } keys %$column_set ];
    }
    my %filter_hash;
    @filter_hash{ @$filter_columns } = @{ $self->slicer( $object, $filter_columns ) };
443

444
445
    my @constraints = ();
    my @values = ();
446
    while(my ($column, $value) = each %filter_hash ) {
447
448
449
450
451
452
453
        if( defined($value) ) {
            push @constraints, "$column = ?";
            push @values, $value;
        } else {
            push @constraints, "$column IS NULL";
        }
    }
454

455
    my $sql = 'SELECT '.($autoinc_id or 1)." FROM $table_name WHERE ".  join(' AND ', @constraints);
456
#warn "check_object_present_in_db_by_content: sql= $sql WITH VALUES (".join(', ', @values).")\n";
457
458
    my $sth = $self->prepare( $sql );
    $sth->execute( @values );
459

460
    my ($return_value) = $sth->fetchrow_array();
461
462
463
464
465
466
467
    $sth->finish;

    return $return_value;
}


sub store {
468
    my ($self, $object_or_list) = @_;
469
470
471
472
473
474

    my $objects = (ref($object_or_list) eq 'ARRAY')     # ensure we get an array of objects to store
        ? $object_or_list
        : [ $object_or_list ];
    return unless(scalar(@$objects));

475
476
    my $table_name              = $self->table_name();
    my $autoinc_id              = $self->autoinc_id();
477
    my $all_storable_columns    = [ grep { $_ ne $autoinc_id } keys %{ $self->column_set() } ];
478
479
480
    my $driver                  = $self->dbc->driver();
    my $insertion_method        = $self->insertion_method;  # INSERT, INSERT_IGNORE or REPLACE
    $insertion_method           =~ s/_/ /g;
481
482
    if($driver eq 'sqlite') {
        $insertion_method =~ s/INSERT IGNORE/INSERT OR IGNORE/ig;
483
484
    } elsif($driver eq 'pgsql') {   # FIXME! temporary hack
        $insertion_method = 'INSERT';
485
    }
486

487
    my %hashed_sth = ();  # do not prepare statements until there is a real need
488

489
490
    my $stored_this_time        = 0;

491
    foreach my $object (@$objects) {
492
            my ($columns_being_stored, $column_key) = $self->keys_to_columns($object);
493
            # warn "COLUMN_KEY='$column_key'\n";
494
495

            my $this_sth;
496

497
498
499
500
                # only prepare (once!) if we get here:
            unless($this_sth = $hashed_sth{$column_key}) {
                    # By using question marks we can insert true NULLs by setting corresponding values to undefs:
                my $sql = "$insertion_method INTO $table_name (".join(', ', @$columns_being_stored).') VALUES ('.join(',', (('?') x scalar(@$columns_being_stored))).')';
501
                # warn "STORE: $sql\n";
502
503
504
                $this_sth = $hashed_sth{$column_key} = $self->prepare( $sql ) or die "Could not prepare statement: $sql";
            }

505
            # warn "STORED_COLUMNS: ".stringify($columns_being_stored)."\n";
506
            my $values_being_stored = $self->slicer( $object, $columns_being_stored );
507
            # warn "STORED_VALUES: ".stringify($values_being_stored)."\n";
508

509
            my $return_code = $this_sth->execute( @$values_being_stored )
510
                    # using $return_code in boolean context allows to skip the value '0E0' ('no rows affected') that Perl treats as zero but regards as true:
511
                or die "Could not store fields\n\t{$column_key}\nwith data:\n\t(".join(',', @$values_being_stored).')';
Leo Gordon's avatar
Leo Gordon committed
512
            if($return_code > 0) {     # <--- for the same reason we have to be explicitly numeric here
513
514
                my $liid = $autoinc_id && $self->dbc->db_handle->last_insert_id(undef, undef, $table_name, $autoinc_id);
                $self->mark_stored($object, $liid );
515
                ++$stored_this_time;
516
517
518
            }
    }

519
520
521
    foreach my $sth (values %hashed_sth) {
        $sth->finish();
    }
522

523
    return ($object_or_list, $stored_this_time);
524
525
526
527
528
529
530
531
}


sub DESTROY { }   # to simplify AUTOLOAD

sub AUTOLOAD {
    our $AUTOLOAD;

532
533
534
535
536
    if($AUTOLOAD =~ /::fetch(_all)?(?:_by_(\w+?))?(?:_HASHED_FROM_(\w+?))?(?:_TO_(\w+?))?$/) {
        my $all             = $1;
        my $filter_string   = $2;
        my $key_string      = $3;
        my $value_column    = $4;
537
538
539
540

        my ($self) = @_;
        my $column_set = $self->column_set();

541
        my $filter_components = $filter_string && [ split(/_AND_/i, $filter_string) ];
542
543
544
545
546
        foreach my $column_name ( @$filter_components ) {
            unless($column_set->{$column_name}) {
                die "unknown column '$column_name'";
            }
        }
547
        my $key_components = $key_string && [ split(/_AND_/i, $key_string) ];
548
        foreach my $column_name ( @$key_components ) {
549
550
551
552
            unless($column_set->{$column_name}) {
                die "unknown column '$column_name'";
            }
        }
553
554
555
        if($value_column && !$column_set->{$value_column}) {
            die "unknown column '$value_column'";
        }
556

557
#        warn "Setting up '$AUTOLOAD' method\n";
558
559
560
561
562
563
564
565
566
        *$AUTOLOAD = sub {
            my $self = shift @_;
            return $self->fetch_all(
                join(' AND ', map { "$filter_components->[$_]='$_[$_]'" } 0..scalar(@$filter_components)-1),
                !$all,
                $key_components,
                $value_column
            );
        };
567
        goto &$AUTOLOAD;    # restart the new method
568

569
    } elsif($AUTOLOAD =~ /::count_all_by_(\w+)$/) {
570
        my $filter_string = $1;
571
572
573
574

        my ($self) = @_;
        my $column_set = $self->column_set();

575
576
577
578
579
        my $filter_components = $filter_string && [ split(/_AND_/i, $filter_string) ];
        foreach my $column_name ( @$filter_components ) {
            unless($column_set->{$column_name}) {
                die "unknown column '$column_name'";
            }
580
        }
581

582
#        warn "Setting up '$AUTOLOAD' method\n";
583
584
585
586
587
588
589
590
        *$AUTOLOAD = sub {
            my $self = shift @_;
            return $self->count_all(
                join(' AND ', map { "$filter_components->[$_]='$_[$_]'" } 0..scalar(@$filter_components)-1),
            );
        };
        goto &$AUTOLOAD;    # restart the new method

591
592
593
594
595
596
597
    } elsif($AUTOLOAD =~ /::remove_all_by_(\w+)$/) {
        my $filter_name = $1;

        my ($self) = @_;
        my $column_set = $self->column_set();

        if($column_set->{$filter_name}) {
598
#            warn "Setting up '$AUTOLOAD' method\n";
599
600
601
602
603
            *$AUTOLOAD = sub { my ($self, $filter_value) = @_; return $self->remove_all("$filter_name='$filter_value'"); };
            goto &$AUTOLOAD;    # restart the new method
        } else {
            die "unknown column '$filter_name'";
        }
604
    } elsif($AUTOLOAD =~ /::update_(\w+)$/) {
605
        my @columns_to_update = split(/_AND_/i, $1);
606
#        warn "Setting up '$AUTOLOAD' method\n";
607
608
609
        *$AUTOLOAD = sub { my ($self, $object) = @_; return $self->update($object, @columns_to_update); };
        goto &$AUTOLOAD;    # restart the new method
    } else {
610
        warn "sub '$AUTOLOAD' not implemented";
611
612
613
614
615
    }
}

1;