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lib/Bio/DB/Taxonomy/sqlite.pm  view on Meta::CPAN

    # one file.  Mayeb ignore it in favor of having full path for db_name?
    my ($dir, $db_name) = ($self->index_directory, $self->db_name);
    if (! -e $db_name || $force) {

        # TODO: we're ignoring index_directory for now, may add support for this
        # down the way
        my $dbh = DBI->connect("dbi:SQLite:dbname=$db_name","","") or die $!;

        $self->debug("Running SQLite version:".$dbh->{sqlite_version}."\n");

        #$dbh->do('PRAGMA synchronous = 0');      # Non transaction safe!!!

        if ($self->cache_size) {
            my $cs = $self->cache_size;
            $self->debug("Setting cache size $cs\n");
            $dbh->do("PRAGMA cache_size = $cs")
        }

        $self->debug("Loading taxon table data\n");
        $self->_init_db($dbh);
        open my $NODES, '<', $nodesfile

lib/Bio/DB/Taxonomy/sqlite.pm  view on Meta::CPAN

        $self->debug("Creating taxon index\n");
        $dbh->do("CREATE INDEX parent_idx ON taxon (parent_id)") or $self->throw($dbh->errstr);
        $self->debug("Creating name index\n");
        $dbh->do("CREATE INDEX name_idx ON names (name)") or $self->throw($dbh->errstr);
        $self->debug("Creating taxon name table index\n");
        $dbh->do("CREATE INDEX taxon_name_idx ON names (taxon_id)") or $self->throw($dbh->errstr);

        $dbh->do("PRAGMA foreign_keys = ON");

        #$dbh->do('PRAGMA synchronous = 1');
        $self->{dbh} = $dbh;
        $self->{'_initialized'} = 1;
    }
    1;
}

# connect the internal db handle
sub _db_connect {
    my $self = shift;
    return if $self->{'_initialized'};