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lib/Bio/EnsEMBL/DBSQL/MiscSetAdaptor.pm  view on Meta::CPAN

 SET:
  foreach my $ms (@misc_sets) {
    if(!ref($ms) || !$ms->isa('Bio::EnsEMBL::MiscSet')) {
      throw("List of MiscSet arguments expected.");
    }

    if($ms->is_stored($db)) {
      warning("MiscSet [".$ms->dbID."] is already stored in this database.");
      next SET;
    }

    $sth->bind_param(1,$ms->code,SQL_VARCHAR);
    $sth->bind_param(2,$ms->name,SQL_VARCHAR);
    $sth->bind_param(3,$ms->description,SQL_LONGVARCHAR);
    $sth->bind_param(4,$ms->longest_feature,SQL_INTEGER);

    my $num_inserted = $sth->execute();

    my $dbID;

    if($num_inserted == 0) {
      # insert failed because set with this code already exists
      my $sth2 = $self->prepare("SELECT misc_set_id from misc_set " .
                                "WHERE code = ?");
      $sth2->bind_param(1,$ms->code,SQL_VARCHAR);
      $sth2->execute();

      ($dbID) = $sth2->fetchrow_array();

      if($sth2->rows() != 1) {
        throw("Could not retrieve or store MiscSet, code=[".$ms->code."]\n".
              "Wrong database user/permissions?");
      }
    } else {
      $dbID = $self->last_insert_id('misc_set_id', undef, 'misc_set');
    }

    $ms->dbID($dbID);
    $ms->adaptor($self);

    # update the internal caches
    $self->{'_id_cache'}->{$dbID} = $ms;
    $self->{'_code_cache'}->{lc($ms->code())} = $ms;
  }

  return;
}

=head2 update

  Arg [1]    : Bio::EnsEMBL::MiscSet $miscset
  Example    : $adaptor->update($miscset)
  Description: Updates this misc_set in the database
  Returntype : int 1 if update is performed, undef if it is not
  Exceptions : throw if arg is not an misc_set object
  Caller     : ?
  Status     : Stable

=cut

sub update {
  my $self = shift;
  my $m    = shift;

  if (!ref($m) || !$m->isa('Bio::EnsEMBL::MiscSet')) {
    throw("Expected Bio::EnsEMBL::MiscSet argument.");
  }

  if(!$m->is_stored($self->db())) {
    return undef;
  }

  my $sth = $self->prepare("UPDATE misc_set ".
			   "SET code =?, name =?, description = ?, max_length = ? ".
			   "WHERE misc_set_id = ?");

  $sth->bind_param(1,$m->code,SQL_VARCHAR);
  $sth->bind_param(2,$m->name,SQL_VARCHAR);
  $sth->bind_param(3,$m->description,SQL_VARCHAR);
  $sth->bind_param(4,$m->longest_feature,SQL_INTEGER);
  $sth->bind_param(5,$m->dbID,SQL_INTEGER);

  $sth->execute();
  $sth->finish();

 # update the internal caches
  $self->{'_id_cache'}->{$m->dbID} = $m;
  $self->{'_code_cache'}->{lc($m->code())} = $m;
}

1;