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

  my $stats_id = $self->fetch_by_statistic($statistic, $attribute)->dbID;

  if (defined $stats_id) {
    $self->update($statistic, $value, $attribute);
  } else {
    my $db = $self->db();
    my $species_id = $db->species_id();

    my $store_genome_sql = q{
    INSERT INTO genome_statistics
       SET statistic = ?,
               value = ?,
          species_id = ?,
           timestamp = now()
    };

    if (defined $attribute) {
      $store_genome_sql .= ", attrib_type_id = ?";
    }

    my $sth = $self->prepare($store_genome_sql);
    $sth->bind_param(1,   $statistic,         SQL_VARCHAR);
    $sth->bind_param(2,   $value,             SQL_INTEGER);
    $sth->bind_param(3,   $species_id,        SQL_INTEGER);

    if (defined $attribute) {
      my $attribute_adaptor = $db->get_AttributeAdaptor();
      my $attribute_object = Bio::EnsEMBL::Attribute->new(-code => $attribute);
      my $attribute_type_id = $attribute_adaptor->_store_type($attribute_object);
      $sth->bind_param(4, $attribute_type_id, SQL_VARCHAR);
    }

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

    $stats_id = $sth->{'mysql_insertid'};
  }

  return $stats_id;

}


=head2 update

  Arg [1]    : Statistic
               The type of statistic to update
  Arg [2]    : Value
               The corresponding value for the statistic
  Arg [3]    : (optional) Attribute
               If more than one value exists for the statistics, it will be distinguished by its attribute
  Example    : $genome_adaptor->update('coding_cnt', 20769);
  Description: Updates an existing genome statistic in the database
  Returntype : none
  Exceptions :
  Caller     : general
  Status     : Stable

=cut

sub update {
  my ($self, $statistic, $value, $attribute) = @_;

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

  my $update_genome_sql = q{
    UPDATE genome_statistics
       SET value = ?,
       timestamp = now()
  };

  if (defined $attribute) {
    $update_genome_sql .= ', attrib_type_id = ?';
  }

  $update_genome_sql .= ' WHERE statistic = ? and species_id = ?';

  my $sth = $self->prepare($update_genome_sql);
  $sth->bind_param(1,   $value,     SQL_INTEGER);

  my $increment = 2;
  if (defined $attribute) {
    my $attribute_adaptor = $db->get_AttributeAdaptor();
    my $attribute_object = Bio::EnsEMBL::Attribute->new(-code => $attribute);
    my $attribute_type_id = $attribute_adaptor->_store_type($attribute_object);
    $sth->bind_param($increment, $attribute_type_id, SQL_VARCHAR);
    $increment++;
  }

  $sth->bind_param($increment++, $statistic, SQL_VARCHAR);
  $sth->bind_param($increment, $db->species_id(), SQL_INTEGER);

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


=head2 _meta_container

  Arg [1]    : none
  Example    : $meta_container = $genome->_meta_container();
  Description: Internal method to return a MetaContainer object for the genome
  Returntype : Bio::EnsEMBL::DBSQL::MetaContainer
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub _meta_container {
  my $self = shift;
  return $self->db->get_adaptor('MetaContainer');
}


=head2 get_version

  Arg [1]    : (optional) assembly version
  Example    : $version = $genome->get_version();
  Description: Getter/Setter for the assembly version