view release on metacpan or  search on metacpan

Das.pm  view on Meta::CPAN

    else {
       warn $request->error;
    }
  }

The is_success() method returns true on a successful request, false
otherwise.  In case of an unsuccessful request, the error() method
will provide additional information on why the request failed The
format is "XXXX human-readable string" as in:

    400 Bad command

The following error strings can be returned:

       400 Bad command
       401 Bad data source
       402 Bad command arguments
       403 Bad reference object
       404 Bad stylesheet
       405 Coordinate error
       410 Unknown host
       411 Couldn't connect
       412 Communications error
       413 Authentication scheme 'xxxx" is not supported
       500 Server error
       501 Unimplemented feature
       502 No X-Das-Version header
       503 Invalid X-Das-Version header
       504 DAS server is too old
       505 No X-Das-Status header
       506 Data decompression failure

To discover which server a request was sent to, you can call its dsn()
method.  This will return the server and data source as a single URL,
e.g.:

   my $dsn = $request->dsn;
   print $dsn,"\n";  # prints 'http://www.wormbase.org/db/das/elegans'

What is returned is actually a L<Bio::Das::DSN> object.  You can call
the object's base() method to return the server part of the DSN, and
its id() method to return the data source:

   my $dsn = $request->dsn;
   print $dsn->base,"\n";  # prints 'http://www.wormbase.org/db/das'
   print $dsn->id,"\n";    # prints 'elegans'

To get the results of from the request, call its results() method.  In
a list context, results() will return a list of the appropriate
objects for the request (a set of L<Bio::Das::Feature> objects for the
features() request a set of L<Bio::Das::Stylesheet> objects for the
stylesheet() request, a set of L<Bio::Das::Type> objects for the
types() request, and a set of raw DNA strings for the dna()
request.)

In a scalar context, results() will return a hashref in which the keys
are the segment strings passed to the request with the B<-segments>
argument and the values are arrayrefs containing the list of results.

There is an equivalence here.  When this code fragment executes, both
$results_hash1 and $results_hash2 will contain the same information.

  my @results = $request->results;
  my $result_hash1 = {};
  for my $r (@results) {
     my $segment = $r->segment;
     push @{$result_hash{$segment}},$r;
  }

  my $result2_hash2 = $request->results;

=head2 Authentication

It may be desirable to access DAS data that is stored in an
authenticating (password protected) server.  Only HTTP Basic
authentication is currently supported by Bio::Das, but you can run the
authentication over an SSL connection, thereby avoiding the risk of
passwords being sniffed.

Authentication information can be passed to the server in either of
two ways:

=over 4

=item In the server's URL

You can provide the username and password in the form:

   http://user:pass@my.das.server.org/cgi-bin/das

Where B<user> and B<pass> are the username and password required for
authentication.

Unless you do with this an SSL (https:) connection, you will get a
warning that using the password in the URL violates the recommendation
in RFC 2396.  You can suppress this warning using the no_rfc_warning()
method:

  $das->no_rfc_warning(1);

=item Using an authentication callback

You can provide a subroutine code reference that returns the username
and password at the time you create the Bio::Das object.  When
accessing a password protected site, Bio::Das will invoke your
callback using information about the request. The callback will return
the appropriate username and password.  You can do whatever you need
to do to get the authentication information, whether accessing an
enterprise database, or popping up a dialog box for the user to
respond to.

=back

To install an authentication callback, pass a coderef to
the B<-auth_callback> argument when calling Bio::Das->new():

  Bio::Das->new(-auth_callback=>\&my_authentication_routine);

The callback will be called with three arguments: