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# $Id$
#
# BioPerl module for Bio::DB::BioSQL::Oracle::TermAdaptorDriver
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Hilmar Lapp <hlapp at gmx.net>
#
# Copyright Hilmar Lapp
#
#
# (c) Hilmar Lapp, hlapp at gmx.net, 2003.
# (c) GNF, Genomics Institute of the Novartis Research Foundation, 2003.
#
# You may distribute this module under the same terms as perl itself.
# Refer to the Perl Artistic License (see the license accompanying this
# software package, or see http://www.perl.com/language/misc/Artistic.html)
# for the terms under which you may use, modify, and redistribute this module.
#
# THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
# WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
# MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
#
# POD documentation - main docs before the code
=head1 NAME
Bio::DB::BioSQL::Oracle::TermAdaptorDriver - DESCRIPTION of Object
=head1 SYNOPSIS
Give standard usage here
=head1 DESCRIPTION
Describe the object here
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
L<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
http://bugzilla.open-bio.org/
=head1 AUTHOR - Hilmar Lapp
Email hlapp at gmx.net
=head1 CONTRIBUTORS
Additional contributors names and emails here
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::DB::BioSQL::Oracle::TermAdaptorDriver;
use vars qw(@ISA);
use strict;
use Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver;
@ISA = qw(Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver);
=head2 remove_synonyms
Title : remove_synonyms
Usage :
Function: Removes all synonyms for an ontology term.
Example :
Returns : TRUE on success, and FALSE otherwise.
Args : The calling persistence adaptor.
The persistent term object for which to remove the synonyms
(a Bio::DB::PersistentObjectI compliant object with defined
primary key).
=cut
sub remove_synonyms{
my ($self,$adp,$obj) = @_;
# delete statement cached?
my $cachekey = "DELETE SYNONYMS";
my $sth = $adp->sth($cachekey);
# if not we need to build it
if(! $sth) {
# we need table name and foreign key
my $table = $self->table_name("TermSynonym");
my $fkname = $self->foreign_key_name($obj->obj);
# build, prepare, and cache the SQL statement
$sth = $self->_build_sth($adp, $cachekey,
"DELETE FROM $table WHERE $fkname = ?");
}
# bind parameters and execute insert
my $dbgmsg = "executing with values (".
$obj->primary_key().") (FK to ".ref($obj->obj).")";
$adp->debug("$cachekey: $dbgmsg\n");
my $rv = $sth->execute($obj->primary_key());
if(! $rv) {
$self->warn("failed to remove term synonyms (".ref($adp)
.") with values (".$obj->primary_key()
.") (FK to ".ref($obj->obj)."):\n".$sth->errstr());
}
return $rv;
}
=head2 store_synonym
Title : store_synonym
Usage :
Function: Stores a synonym for an ontology term.
Example :
Returns : TRUE on success, and FALSE otherwise.
Args : The calling persistence adaptor.
The persistent term object for which to store the synonym
(a Bio::DB::PersistentObjectI compliant object with defined
primary key).
The synonym to store (a scalar).
=cut
sub store_synonym{
my ($self,$adp,$obj,$syn) = @_;
# insert and look-up statements cached?
my $icachekey = "INSERT SYNONYM";
my $isth = $adp->sth($icachekey);
# if not we need to build them
if(! $isth) {
# we need table name, foreign key, and slot map
my $table = $self->table_name("TermSynonym");
my $fkname = $self->foreign_key_name($obj->obj);
my $colmap = $self->slot_attribute_map($table);
# build, prepare, and cache the SQL statements
$isth = $self->_build_sth($adp, $icachekey,
"INSERT INTO $table (".
join(", ", $colmap->{'synonym'}, $fkname).
") VALUES (?, ?)");
}
# bind parameters and execute insert
my $dbgmsg = "executing with values ($syn, ".
$obj->primary_key().") (synonym, FK to ".ref($obj->obj).")";
$adp->debug("$icachekey: $dbgmsg\n");
my $rv = $isth->execute($syn, $obj->primary_key());
if(! $rv) {
# this might be a UK failure, not a bad statement error
if (index($isth->errstr(), "ORA-00001") >= 0) {
# we actually don't need to execute a look-up here because the
# synonym is not an object and hence has no primary key itself
$rv = "0E0"; # evaluates to TRUE, but numerically equals zero
} else {
$self->warn("failed to store term synonym (".ref($adp)
.") with values ($syn) (FK ".$obj->primary_key()
." to ".ref($obj->obj)."):\n"
.$isth->errstr());
}
}
return $rv;
}
sub _build_sth{
my ($self,$adp,$cachekey,$sql) = @_;
# prepare and cache
$adp->debug("$cachekey: preparing: $sql\n");
my $sth = $adp->dbh->prepare($sql);
$self->throw("failed to prepare \"$sql\": ".$adp->dbh->errstr)
unless $sth;
$adp->sth($cachekey,$sth);
return $sth;
}
=head2 get_synonyms
Title : get_synonyms
Usage :
Function: Retrieves the synonyms for an ontology term and adds them
the term's synonyms.
Example :
Returns : TRUE on success, and FALSE otherwise.
Args : The calling persistence adaptor.
The persistent term object for which to retrieve the
synonyms (a Bio::DB::PersistentObjectI compliant object
with defined primary key).
=cut
sub get_synonyms{
my ($self,$adp,$obj) = @_;
# look-up statement cached?
my $cachekey = "SELECT SYNONYMS";
my $sth = $adp->sth($cachekey);
# if not we need to build it
if(! $sth) {
# we need table name, foreign key, and slot map
my $table = $self->table_name("TermSynonym");
my $fkname = $self->foreign_key_name($obj->obj);
my $colmap = $self->slot_attribute_map($table);
# build, prepare, and cache the SQL statement
$sth = $self->_build_sth($adp, $cachekey,
"SELECT ".$colmap->{'synonym'}.
" FROM $table WHERE $fkname = ?");
}
# bind parameters and execute select
my $dbgmsg = "executing with values (".
$obj->primary_key().") (FK to ".ref($obj->obj).")";
$adp->debug("$cachekey: $dbgmsg\n");
my $rv = $sth->execute($obj->primary_key());
$self->warn("failed to execute $cachekey: ".$sth->errstr) unless $rv;
while(my $row = $sth->fetchrow_arrayref()) {
$obj->add_synonym($row->[0]);
}
return $rv;
}
=head2 bind_param
Title : bind_param
Usage :
Function: Binds a parameter value to a prepared statement.
We override this in order to possibly truncate term
definitions longer than 4000 characters, the limit of
Oracle's VARCHAR2 data type. Note that this problem does
not exist with Pg's and mysql's text types.
Example :
Returns : the return value of the DBI::bind_param() call
Args : the DBI statement handle to bind to
the index of the column (1-based)
the value to bind
additional arguments to be passed to the sth->bind_param call
=cut
sub bind_param{
my ($self,$sth,$i,$val,@bindargs) = @_;
# definition is the 3rd value to bind
if (($i == 3) && defined($val) && (length($val) > 4000)) {
$self->warn("term definition is "
.length($val)." chars long, need to truncate to 4000");
$val = substr($val,0,4000);
}
return $self->SUPER::bind_param($sth,$i,$val,@bindargs);
}
1;
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