Bio-Biblio

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lib/Bio/Biblio.pm  view on Meta::CPAN

    # this is called only the first time when somebody calls: 'new
    # Bio::Biblio (...)', and it actually loads a 'real-work-doing'
    # module and call this new() method again (unless the loaded
    # module has its own new() method)

    } else {
        my %param = @args;
        @param { map { lc $_ } keys %param } = values %param; # lowercase keys
        my $access =
            $param {'-access'} ||
            $class->_guess_access ( $param {'-location'} ) ||
            'soap';
        $access = "\L$access";  # normalize capitalization to lower case

        # load module with the real implementation - as defined in $access
        return unless (&_load_access_module ($access));

        # this will call this same method new() - but rather its the
        # upper (object) branche
        return "Bio::DB::Biblio::$access"->new (@args);
    }

lib/Bio/Biblio.pm  view on Meta::CPAN

    return 1;
}

# -----------------------------------------------------------------------------


# this is kept here for the future when more access protocols
# (e.g. CORBA) may be available for accessing bibliographic query
# services

sub _guess_access {
#    my ($class, $location) = @_;
    return 'soap';
}

1;

__END__
=pod

=encoding utf-8

lib/Bio/Biblio.pm  view on Meta::CPAN

 Args    : 'access' should contain the last part of the
           name of a module who does the real implementation

It does (in run-time) a similar thing as

   require Bio::DB::Biblio::$access

It prints an error on STDERR if it fails to find and load the module
(for example, because of the compilation errors in the module).

=head2 _guess_access

 Usage   : $class->_guess_access ($location)
 Returns : string with a guessed access protocol (e.g. 'soap')
 Args    : 'location' defines where to find a bibliographic service
           in a protocol-dependent manner (e.g. for SOAP it is
           a URL of a bibliographic WebService)

It makes an expert guess what kind of access/transport protocol should
be used based on the I<location> of the service (e.g. if the
I<location> looks like an IOR then the access protocol is probably
CORBA).

=head1 OVERVIEW OF CLASSES AND PACKAGES

=over

=item L<Bio::Biblio>

lib/Bio/Biblio/IO.pm  view on Meta::CPAN

        return $self;

    # this is called only the first time when somebody calls: 'new
    # Bio::Biblio::IO (...)', and it actually loads a 'real-work-doing'
    # module and call this new() method again (unless the loaded
    # module has its own new() method)
    } else {
        my %param = @args;
        @param{ map { lc $_ } keys %param } = values %param; # lowercase keys
        my $format = $param{'-format'} ||
            $class->_guess_format( $param{-file} || $ARGV[0] ) ||
                'medlinexml';
        $format = "\L$format";  # normalize capitalization to lower case

        # load module with the real implementation - as defined in $format
        return unless (&_load_format_module ($format));

        # this will call this same method new() - but rather its
        # upper (object) branche
        return "Bio::Biblio::IO::$format"->new(@args);
    }

lib/Bio/Biblio/IO.pm  view on Meta::CPAN

Exception $@
For more information about the Biblio system please see the Bio::Biblio::IO docs.
END
        ;
        return;
    }
    return 1;
}


sub _guess_format {
    my $class = shift;
    return unless $_ = shift;
    return 'medlinexml'   if (/\.(xml|medlinexml)$/i);
    return;
}


sub DESTROY {
    my $self = shift;

lib/Bio/Biblio/IO.pm  view on Meta::CPAN

 Args    : 'format' should contain the last part of the
           name of a module who does the real implementation

It does (in run-time) a similar thing as

   require Bio::Biblio::IO::$format

It throws an exception if it fails to find and load the module
(for example, because of the compilation errors in the module).

=head2 _guess_format

 Usage   : $class->_guess_format ($filename)
 Returns : string with a guessed format of the input data (e.g. 'medlinexml')
 Args    : a file name whose extension can help to guess its format

It makes an expert guess what kind of data are in the given file
(but be prepare that $filename may be empty).

=head1 SEE ALSO

=over 4

=item *

An example script F<eg/biblio-soap.pl>