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

    $dbID = $new_analysis->dbID();
    $analysis->created( $new_analysis->created() );
  }
  
  $dbID ||= $self->last_insert_id('analysis_id', undef, 'analysis');
  $sth->finish();

  # store description and display_label
  if( defined( $analysis->description() ) || defined( $analysis->display_label() )|| defined( $analysis->web_data() )) {
      $self->_store_description($analysis, $dbID);
  }


  $self->{_cache}->{$dbID} = $analysis;
  $self->{_logic_name_cache}{lc($analysis->logic_name)} = $analysis;

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

  return $dbID;
}


sub _store_description {
  my ($self, $analysis, $dbID) = @_;

  my $insert_ignore = $self->insert_ignore_clause();
  my $sth = $self->prepare(
    "${insert_ignore} INTO analysis_description (analysis_id, display_label, description, displayable, web_data) " .
    "VALUES (?,?,?,?,?)"
    );

  my $display_label = $analysis->display_label();
  $display_label = '' unless defined $display_label; # SQLite doesn't ignore NOT NULL errors

  $sth->bind_param(1,$dbID,SQL_INTEGER);
  $sth->bind_param(2,$display_label,SQL_VARCHAR);
  $sth->bind_param(3,$analysis->description,SQL_LONGVARCHAR);
  $sth->bind_param(4,$analysis->displayable,SQL_TINYINT);
  $sth->bind_param(5,$analysis->web_data,SQL_LONGVARCHAR);
  $sth->execute();

  $sth->finish();
  return;
}


=head2 update

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

=cut

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

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

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

  my $sth = $self->prepare
    ("UPDATE analysis " .
     "SET created = ?, logic_name = ?, db = ?, db_version = ?, db_file = ?, ".
     "    program = ?, program_version = ?, program_file = ?,  ".
     "    parameters = ?, module = ?, module_version = ?, ".
     "    gff_source = ?, gff_feature = ? " .
     "WHERE analysis_id = ?");



  $sth->bind_param(1,$a->created,SQL_DATETIME);
  $sth->bind_param(2,$a->logic_name,SQL_VARCHAR);
  $sth->bind_param(3,$a->db,SQL_VARCHAR);
  $sth->bind_param(4,$a->db_version,SQL_VARCHAR);
  $sth->bind_param(5,$a->db_file,SQL_VARCHAR);
  $sth->bind_param(6,$a->program,SQL_VARCHAR);
  $sth->bind_param(7,$a->program_version,SQL_VARCHAR);
  $sth->bind_param(8,$a->program_file,SQL_VARCHAR);
  $sth->bind_param(9,$a->parameters,SQL_VARCHAR);
  $sth->bind_param(10,$a->module,SQL_VARCHAR);
  $sth->bind_param(11,$a->module_version,SQL_VARCHAR);
  $sth->bind_param(12,$a->gff_source,SQL_VARCHAR);
  $sth->bind_param(13,$a->gff_feature,SQL_VARCHAR);
  $sth->bind_param(14,$a->dbID,SQL_INTEGER);

  $sth->execute();

  $sth->finish();

  # also update description & display label - may need to create these if
  # not already there
  $sth = $self->prepare("SELECT description FROM analysis_description WHERE analysis_id= ?");
  $sth->execute($a->dbID);
  if ($sth->fetchrow_hashref) { # update if exists
      $sth = $self->prepare
      ("UPDATE analysis_description SET description = ?, display_label = ?, displayable = ?, web_data = ? WHERE analysis_id = ?");
      $sth->bind_param(1,$a->description,SQL_LONGVARCHAR);     
      $sth->bind_param(2,$a->display_label(),SQL_VARCHAR);
      $sth->bind_param(3,$a->displayable,SQL_TINYINT);
      $sth->bind_param(4,$a->web_data,SQL_LONGVARCHAR);
      $sth->bind_param(5,$a->dbID,SQL_INTEGER);
      $sth->execute();

  } else { # create new entry

    if( $a->description() || $a->display_label() || $a->web_data) {
        $self->_store_description($a, $a->dbID);
    }