view release on metacpan or  search on metacpan

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

    $params = [];
  }
  unshift(@{$params}, $self->db()->species_id());
  
  my $csa = $self->db()->get_CoordSystemAdaptor();
  my $aa = $self->db()->get_AnalysisAdaptor();
  
  return $self->dbc()->sql_helper()->execute(-SQL => $sql, -PARAMS => $params, -CALLBACK => sub {
    my ($row) = @_;
    my ($data_file_id, $coord_system_id, $analysis_id, $name, $version_lock, $absolute, $url, $file_type) = @{$row};
    my $hash = {
      dbID          => $data_file_id,
      adaptor       => $self,
      coord_system  => $csa->fetch_by_dbID($coord_system_id),
      analysis      => $aa->fetch_by_dbID($analysis_id),
      name          => $name,
      version_lock  => $version_lock,
      absolute      => $absolute,
      file_type     => $file_type,
    };
    $hash->{url} = $url if $url;
    return Bio::EnsEMBL::DataFile->new_fast($hash);
  });
}

sub store {
  my ($self, $df) = @_;
  
  assert_ref($df, 'Bio::EnsEMBL::DataFile', 'datafile');
  
  if ($df->is_stored($self->db())) {
    return $df->dbID();
  }
  
  throw 'Analysis is not defined for this data file' if ! defined $df->analysis();
  throw 'Coord system is not defined for this data file' if ! defined $df->coord_system();
  
  my $sql = <<'SQL';
INSERT INTO data_file (coord_system_id, analysis_id, name, version_lock, absolute, url, file_type)
VALUES (?,?,?,?,?,?,?)
SQL
  my $params = [
    [$df->coord_system()->dbID(), SQL_INTEGER], 
    [$df->analysis()->dbID(), SQL_INTEGER],
    [$df->name(), SQL_VARCHAR],
    [$df->version_lock(), SQL_INTEGER],
    [$df->absolute(), SQL_INTEGER],
    [$df->url(), SQL_VARCHAR],
    [$df->file_type(), SQL_VARCHAR],
  ];
  $self->dbc()->sql_helper()->execute_update(-SQL => $sql, -PARAMS => $params, -CALLBACK => sub {
    my ( $sth, $dbh ) = @_;
    $df->dbID($self->last_insert_id());
    return;
  });
  $df->adaptor($self);
  
  return $df->dbID();
}

sub update {
  my ($self, $df) = @_;
  
  assert_ref($df, 'Bio::EnsEMBL::DataFile', 'datafile');
  
  if (! $df->is_stored($self->db())) {
    $self->store($df);
    return;
  }
  
  my $sql = <<'SQL';
UPDATE data_file SET coord_system_id =?, analysis_id=?, name=?, version_lock=?, absolute=?, url=?, file_type=?
WHERE data_file_id =?
SQL
  my $params = [
    [$df->coord_system()->dbID(), SQL_INTEGER], 
    [$df->analysis()->dbID(), SQL_INTEGER],
    [$df->name(), SQL_VARCHAR],
    [$df->version_lock(), SQL_INTEGER],
    [$df->absolute(), SQL_INTEGER],
    [$df->url(), SQL_VARCHAR],
    [$df->file_type(), SQL_VARCHAR],
    [$df->dbID(), SQL_INTEGER],
  ];
  $self->dbc()->sql_helper()->execute_update(-SQL => $sql, -PARAMS => $params);
  return;
}

sub delete {
  my ($self, $df) = @_;
  
  assert_ref($df, 'Bio::EnsEMBL::DataFile', 'datafile');
  
  if (! $df->is_stored($self->db())) {
    throw "Cannot delete the data file if it has not already been stored in this database";
  }
  
  $self->dbc()->sql_helper()->execute_update(
    -SQL => 'DELETE from data_file where data_file_id =?', 
    -PARAMS => [[$df->dbID(), SQL_INTEGER]],
  );
  
  return;
}

sub _tables {
  my ($self) = @_;
  return (
    [qw/data_file df/]
  );
}

1;