Lincoln D. Stein > Bio-Das-1.06 > Bio::Das

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Module Version: 1.06   Source   Latest Release: Bio-Das-1.17

NAME ^

Bio::Das - Interface to Distributed Annotation System

SYNOPSIS ^

  use Bio::Das;

   # SERIAL API
   my $das = Bio::Das->new(-source => 'http://www.wormbase.org/db/das',
                           -dsn    => 'elegans',
                           -aggregators => ['primary_transcript','clone']);
   my $segment  = $das->segment('Chr1');
   my @features = $segment->features;
   my $dna      = $segment->dna;

  # PARALLEL API
  # create a new DAS agent with a timeout of 5 sec
  my $das = Bio::Das->new(5);

  # fetch features from wormbase live and development servers spanning two segments on chromosome I
  my @request = $das->features(-dsn     => ['http://www.wormbase.org/db/das/elegans',
                                            'http://dev.wormbase.org/db/das/elegans',
                                           ],
                               -segment => ['I:1,10000',
                                            'I:10000,20000'
                                           ]
                              );

  for my $request (@request) {
    if ($request->is_success) {
      print "\nResponse from ",$request->dsn,"\n";
      my $results = $request->results;
      for my $segment (keys %$results) {
        my @features = @{$results->{$segment}};
        print "\t",join ' ',$segment,@features,"\n";
      }
    }

    else { #error
      warn $request->dsn,": ",$request->error,"\n";
    }
  }

  # Same thing, but using a callback:
  $das->features(-dsn     => ['http://www.wormbase.org/db/das/elegans',
                              'http://dev.wormbase.org/db/das/elegans',
                              ],
                 -segment => ['I:1,10000',
                              'I:10000,20000'
                             ],
                 -callback => sub { my $feature = shift;
                                    my $segment = $feature->segment;
                                    my ($start,$end) = ($feature->start,$feature->end);
                                    print "$segment => $feature ($start,$end)\n";
                                  }
                               );

DESCRIPTION ^

Bio::Das provides access to genome sequencing and annotation databases that export their data in Distributed Annotation System (DAS) format version 1.5. This system is described at http://biodas.org. Both unencrypted (http:) and SSL-encrypted (https:) DAS servers are supported. (To run SSL, you will need IO::Socket::SSL and Net::SSLeay installed).

The components of the Bio::Das class hierarchy are:

Bio::Das

This class performs I/O with the DAS server, and is responsible for generating DAS requests. At any time, multiple requests to different DAS servers can be running simultaneously.

Bio::Das::Request

This class encapsulates a request to a particular DAS server. After execution of the request, the response can be recovered from the object as well. Methods allow you to return the status of the request, the error message if any, and the data results.

Bio::Das::Segment

This encapsulates information about a segment on the genome, and contains information on its start, end and length.

Bio::Das::Feature

This provides information on a particular feature of a Bio::Das::Segment, such as its type, orientation and score.

Bio::Das::Type

This class contains information about a feature's type, and is a holder for an ontology term.

Bio::Das::DSN

This class contains information about a DAS data source.

Bio::Das::Stylesheet

This class contains information about the stylesheet for a DAS source.

PARALLEL AND SERIAL APIs

Bio::Das supports two distinct APIs. One is a parallel API which allows you to make Das requests on two or more servers simultaneously. This is highly efficient, but the API is slightly more difficult to use. The other is a serial API which supports only a single request on a single service. It is recommended for simple scripts or for those where performance is not at a premium.

The two APIs use the same objects. You select which API to use when you create the Das object with Bio::Das->new().

OBJECT CREATION

The public Bio::Das constructor is new(). It is used both for the parallel and serial APIs.

Serial API object construction:

$das = Bio::Das->new(-server => $url, -dsn => $dsn, -aggregators=>\@aggregators);

Clients that will be accessing a single server exclusively can indicate that they wish to use the serial APi by passing the -server argument. The argument for -server is the base name of the DAS server (e.g. http://www.wormbase.org/db/das). You may also select the data source to use (e.g. "elegans") by passing the -dsn argument. -aggregators is a list of aggregators as described earlier.

The optional -proxy argument will initialize the Bio::Das object with an HTTP or HTTPS proxy (see also the proxy() method below).

$das = Bio::Das->new('http://das.server/cgi-bin/das',$dsn,$aggregators)

Shortcut for the above.

Parallel API object construction:

$das = Bio::Das->new(-timeout => $timeout, -auth_callback => $authentication_callback, -aggregators => \@aggregators)

Create a new Bio::Das object, with the indicated timeout and optional callback for authentication. The timeout will be used to decide when a server is not responding and to return a "can't connect" error. Its value is in seconds, and can be fractional (most systems will provide millisecond resolution). The authentication callback will be invoked if the remote server challenges Bio::Das for authentication credentials.

Aggregators are used to build multilevel hierarchies out of the raw features in the DAS stream. For a description of aggregators, see Bio::DB::GFF, which uses exactly the same aggregator system as Bio::Das.

The optional -proxy argument will initialize the Bio::Das object with an HTTP or HTTPS proxy (see also the proxy() method below).

If successful, this method returns a Bio::Das object.

$das = Bio::Das->new($timeout [,$authentication_callback])

Shortcut for the above.

ACCESSOR METHODS

Once created, the Bio::Das object provides the following accessor methods:

$proxy = $das->proxy([$new_proxy])

Get or set the proxy to use for accessing indicated servers. Only HTTP and HTTPS proxies are supported at the current time.

$callback = $das->auth_callback([$new_callback])

Get or set the callback to use when authentication is required. See the section "Authentication" for more details.

$timeout = $das->timeout([$new_timeout])

Get or set the timeout for slow servers.

$error = $das->error

Get a string that describes the last error the module encountered whie using the serial API. If you are using the parallel API, then use the request object's error() method to retrieve the error message from the corresponding request.

$debug = $das->debug([$debug_flag])

Get or set a flag that will turn on verbose debugging messages.

$das->add_aggregator($aggregator)

Aggregators allow you to dynamically build up more multipart features from the simple one-part that are returned by Das servers. The concept of aggregation was introduced in the Bio::DB::GFF module, and is completely compatible with the Bio::Das implementation. See Bio::DB::GFF and Bio::DB::GFF::Aggregator for information on how to create and use aggregators.

The add_aggregator() method will append an aggregator to the end of the list of registered aggregators. Three different argument types are accepted:

  1) a Bio::DB::GFF::Aggregator object -- will be added
  2) a string in the form "aggregator_name{subpart1,subpart2,subpart3/main_method}"
         -- will be turned into a Bio::DB::GFF::Aggregator object (the /main_method
        part is optional).
  3) a valid Perl token -- will be turned into a Bio::DB::GFF::Aggregator
        subclass, where the token corresponds to the subclass name.
$das->aggregators([@new_aggregators]);

This method will get or set the list of aggregators assigned to the database. If 1 or more arguments are passed, the existing set will be cleared.

$das->clear_aggregators

This method will clear the aggregators stored in the database object. Use aggregators() or add_aggregator() to add some back.

DATA FETCHING METHODS - SERIAL API

We will document that serial API first, followed by the parallel API. Do not be confused by the fact is that both serial and parallel APIs have the same method names. The behavior of the methods are determined solely by whether the -server argument was provided to Bio::Das->new() during object construction.

@dsn = $das->sources

Return a list of data sources available from this server. This is one of the few methods that can be called before setting the data source.

$segment = $das->segment($id)
$segment = $das->segment(-ref => $reference [,@args]);

The segment() method returns a new Bio::Das::Segment object, which can be queried for information related to a sequence segment. There are two forms of this call. In the single-argument form, you pass segment() an ID to be used as the reference sequence. Sequence IDs are server-specific (some servers will accept genbank accession numbers, others more complex IDs such as Locus:unc-9). The method will return a Bio::Das::Segment object containing a region of the genomic corresponding to the ID.

Once you fetch the segment, you can use it to fetch the features that overlap that segment, or the DNA corresponding to the segment. For example:

   my @features = $segment->features();
   my $dna      = $segment->dna();

See Bio::Das::Segment for more details.

Instead of a segment ID, you may use a previously-created Bio::Das::Segment object, in which case a copy of the segment will be returned to you. You can then adjust its start and end positions.

In the multiple-argument form, you pass a series of argument/value pairs:

  Argument   Value                   Default
  --------   -----                   -------

  -ref       Reference ID            none
  -segment   Bio::Das::Segment obj   none
  -start     Starting position       1
  -end       Ending position         length of ref ID
  -offset    Starting position       0
             (0-based)
  -length    Length of segment       length of ref ID

The -ref argument is required, and indicates the ID of the genomic segment to retrieve. -segment is optional, and can be used to use a previously-created Bio::Das::Segment object as the reference point instead. If both arguments are passed, -segment supersedes -ref.

-start and -end indicate the start and stop of the desired genomic segment, relative to the reference ID. If not provided, they default to the start and stop of the reference segment. These arguments use 1-based indexing, so a -start of 0 positions the segment one base before the start of the reference.

-offset and -length arguments are alternative ways to indicate a segment using zero-based indexing. It is probably not a good to mix the two calling styles, but if you do, be aware that -offset supersedes -start and -length supersedes -stop.

Note that no checking of the validity of the passed reference ID will be performed until you call the segment's features() or dna() methods.

@segments = $das->get_feature_by_name(-name=>$name [,-class=>$class]);

This method implements the DAS feature request using parameters that will translate a feature name into one or more segments. This can be used to retrieve the section of a genome that is occupied by a particular feature. If the feature name matches multiple features in discontinuous parts of the genome, this call may return multiple segments. Once you have a segment, you can call its features() method to get information about the features that overlap this region.

The optional -class argument is provided to deal with servers that have namespaced their features using a colon. $das->get_feature_by_name(-name=>'foo',-class=>'bar') is exactly equivalent to $das->get_feature_by_name(-name=>'bar:foo').

Because this method is misnamed (it returns segments, not features), it is also known as feature2segment().

The method can also be called using the shortcut syntax get_feature_by_name($name).

@entry_points = $das->entry_points

The entry_points() method returns an array of Bio::Das::Segment objects that have been designated "entry points" by the DAS server. Also see the Bio::Das::Segment->entry_points() method.

$stylesheet = $das->stylesheet

Return the stylesheet from the remote DAS server. The stylesheet contains suggestions for the visual format for the various features provided by the server and can be used to translate features into glyphs. The object returned is a Bio::Das::Stylesheet object.

@types = $das->types

This method returns a list of all the annotation feature types served by the DAS server. The return value is an array of Bio::Das::Type objects.

DATA FETCHING METHODS - PARALLEL API

The following methods accept a series of arguments, contact the indicated DAS servers, and return a series of request objects from which you can learn the status of the request and fetch the results.

Parallel API:

@request = $das->dsn(@list_of_urls)

The dsn() method accepts a list of DAS server URLs and returns a list of request objects containing the DSNs provided by each server.

The request objects will indicate whether each request was successful via their is_success() methods. For your convenience, the request object is automagically stringified into the requested URL. For example:

 my $das = Bio::Das->new(5);  # timeout of 5 sec
 my @response = $das->dsn('http://stein.cshl.org/perl/das',
                         'http://genome.cse.ucsc.edu/cgi-bin/das',
                         'http://user:pass@www.wormbase.org/db/das',
                         'https://euclid.well.ox.ac.uk/cgi-bin/das',
                        );

 for my $url (@response) {
   if ($url->is_success) {
     my @dsns = $url->results;
     print "$url:\t\n";
     foreach (@dsns) {
       print "\t",$_->url,"\t",$_->description,"\n";
     }
   } else {
     print "$url: ",$url->error,"\n";
   }
 }

Each element in @dsns is a Bio::Das::DSN object that can be used subsequently in calls to features(), types(), etc. For example, when this manual page was written, the following was the output of this script.

 http://stein.cshl.org/perl/das/dsn:    
 http://stein.cshl.org/perl/das/chr22_transcripts       This is the EST-predicted transcripts on...

 http://servlet.sanger.ac.uk:8080/das:  
 http://servlet.sanger.ac.uk:8080/das/ensembl1131   The latest Ensembl database 

 http://genome.cse.ucsc.edu/cgi-bin/das/dsn:    
 http://genome.cse.ucsc.edu/cgi-bin/das/hg8     Human Aug. 2001 Human Genome at UCSC
 http://genome.cse.ucsc.edu/cgi-bin/das/hg10    Human Dec. 2001 Human Genome at UCSC
 http://genome.cse.ucsc.edu/cgi-bin/das/mm1     Mouse Nov. 2001 Human Genome at UCSC
 http://genome.cse.ucsc.edu/cgi-bin/das/mm2     Mouse Feb. 2002 Human Genome at UCSC
 http://genome.cse.ucsc.edu/cgi-bin/das/hg11    Human April 2002 Human Genome at UCSC
 http://genome.cse.ucsc.edu/cgi-bin/das/hg12    Human June 2002 Human Genome at UCSC
 http://user:pass@www.wormbase.org/db/das/dsn:  
 http://user:pass@www.wormbase.org/db/das/elegans     This is the The C. elegans genome at CSHL
 
 https://euclid.well.ox.ac.uk/cgi-bin/das/dsn:  
 https://euclid.well.ox.ac.uk/cgi-bin/das/dicty         Test annotations
 https://euclid.well.ox.ac.uk/cgi-bin/das/elegans       C. elegans annotations on chromosome I & II
 https://euclid.well.ox.ac.uk/cgi-bin/das/ensembl       ensembl test annotations
 https://euclid.well.ox.ac.uk/cgi-bin/das/test          Test annotations
 https://euclid.well.ox.ac.uk/cgi-bin/das/transcripts   transcripts test annotations

Notice that the DSN URLs always have the format:

 http://www.wormbase.org/db/das/$DSN
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

In which the ^^^ indicated part is identical to the server address.

@request = $das->types(-dsn=>[$dsn1,$dsn2],@other_args)

The types() method asks the indicated servers to return the feature types that they provide. Arguments are name-value pairs:

  Argument      Description
  --------      -----------

  -dsn          A DAS DSN, as returned by the dsn() call.  You may
                also provide a simple string containing the DSN URL.
                To make the types() request on multiple servers, pass an
                array reference containing the list of DSNs.

  -segment      (optional) An array ref of segment objects.  If provided, the
                list of types will be restricted to the indicated segments.

  -category     (optional) An array ref of type categories.  If provided,
                the list of types will be restricted to the indicated
                categories.

  -enumerate    (optional) If true, the server will return the count of
                each type.  The count can be retrieved using the 
                L<Bio::Das::Type> objects' count() method.

  -callback     (optional) Specifies a subroutine to be invoked on each
                type object received.

Segments have the format: "seq_id:start,end". If successful, the request results() method will return a list of Bio::Das::Type objects.

If a callback is specified, the code ref will be invoked with two arguments. The first argument is the Bio::Das::Segment object, and the second is an array ref containing the list of types present in that segment. If no -segment argument was provided, then the callback will be invoked once with a dummy segment (a version, but no seq_id, start or end), and an arrayref containing the types. If a callback is specified, then the @request array will return the status codes for each request, but invoking results() will return empty.

@request = $das->entry_points(-dsn=>[$dsn1,$dsn2],@other_args)

Invoke an entry_points request. Arguments are name-value pairs:

  Argument      Description
  --------      -----------

  -dsn          A DAS DSN, as returned by the dsn() call.  You may
                also provide a simple string containing the DSN URL.
                To make the types() request on multiple servers, pass an
                array reference containing the list of DSNs.

  -callback     (optional) Specifies a subroutine to be invoked on each
                segment object received.

If a callback is specified, then the @request array will contain the status codes for each request, but the results() method will return empty.

Successful requests will return a set of Bio::Das::Segment objects.

@request = $das->features(-dsn=>[$dsn1,$dsn2],@other_args)

Invoke a features request to return a set of Bio::Das::Feature objects. The -dsn argument is required, and may point to a single DSN or to an array ref of several DSNs. Other arguments are optional:

  Argument      Description
  --------      -----------

  -dsn          A DAS DSN, as returned by the dsn() call.  You may
                also provide a simple string containing the DSN URL.
                To make the types() request on multiple servers, pass an
                array reference containing the list of DSNs.

  -segment      A single segment, or an array ref containing
                several segments.  Segments are either Bio::Das::Segment
                objects, or strings of the form "seq_id:start,end".

  -type         (optional) A single feature type, or an array ref containing
                several feature types.  Types are either Bio::Das::Type
                objects, or plain strings.

  -category     (optional) A single feature type category, or an array ref
                containing several categories.  Category names are described
                in the DAS specification.

  -feature_id   (optional) One or more feature IDs.  The server will return
                the list of segment(s) that contain these IDs.  You will
                need to check with the data provider for the proper format
                of the IDs, but the style "class:ID" is common.  This will
                be replaced in the near future by LSID-style IDs.  Also note
                that only servers compliant with the 1.52 version of the
                spec will honor this.

  -group_id     (optional) One or more group IDs.  The server will return
                the list of segment(s) that contain these IDs.  You will
                need to check with the data provider for the proper format
                of the IDs, but the style "class:ID" is common.  This will
                be replaced in the near future by LSID-style IDs.  Also note
                that only servers compliant with the 1.52 version of the
                spec will honor this.

  -callback     (optional) Specifies a subroutine to be invoked on each
                Bio::Das::Feature object received.

  -segment_callback (optional) Specifies a subroutine to be invoked on each
                    Segment that is retrieved.

  -iterator     (optional)  If true, specifies that an iterator should be
                returned rather than a list of features.

The features() method returns a list of Bio::Das::Request objects. There will be one request for each DAS DSN provided in the -dsn argument. Requests are returned in the same order that they were passed to -dsn, but you can also query the Bio::Das::Request object to determine which server processed the request. See Fetching Results for details. If you happen to call this method in a scalar context, it will return the first request, discarding the rest.

If a callback (-callback or -segment_callback) is specified, then the @request array will contain the status codes for each request, but results() will return empty.

The subroutine specified by -callback will be invoked every time a feature is encountered. The code will be passed a single argument consisting of a Bio::Das::Feature object. You can find out what segment this feature is contained within by executing the object's segment() method.

The subroutine specified by -segment_callback will be invoked every time one of the requested segments is finished. It will be invoked with two arguments consisting of the name of the segment and an array ref containing the list of Bio::Das::Feature objects contained within the segment.

If both -callback and -segment_callback are specified, then the first subroutine will be invoked for each feature, and the second will be invoked on each segment *AFTER* the segment is finished. In this case, the segment processing subroutine will be passed an empty list of features.

Note, if the -segment argument is not provided, some servers will provide all the features in the database.

The -iterator argument is a true/false flag. If true, the call will return a Bio::Das::FeatureIterator object. This object implements a single method, next_seq(), which returns the next Feature. Example:

   $iterator = $das->features(-dsn=>[$dsn1,$dsn2],-iterator=>1);
   while (my $feature = $iterator->next_seq) {
     my $dsn  = $feature->segment->dsn;
     my $type = $feature->type;
     print "got a $type from $dsn\n";
   }
@request = $das->dna(-dsn=>[$dsn1,$dsn2],@other_args)

Invoke a features request to return a DNA string. The -dsn argument is required, and may point to a single DSN or to an array ref of several DSNs. Other arguments are optional:

  Argument      Description
  --------      -----------

  -dsn          A DAS DSN, as returned by the dsn() call.  You may
                also provide a simple string containing the DSN URL.
                To make the types() request on multiple servers, pass an
                array reference containing the list of DSNs.

  -segment      (optional) A single segment, or an array ref containing
                several segments.  Segments are either Bio::Das::Segment
                objects, or strings of the form "seq_id:start,end".

  -callback     (optional) Specifies a subroutine to be invoked on each
                DNA string received.

-dsn, -segment and -callback have the same meaning that they do in similar methods.

@request = $das->stylesheet(-dsn=>[$dsn1,$dsn2],@other_args)

Invoke a stylesheet request to return the Bio::Das::Stylesheet object. The -dsn argument is required, and may point to a single DSN or to an array ref of several DSNs. Other arguments are optional:

  Argument      Description
  --------      -----------

  -dsn          A DAS DSN, as returned by the dsn() call.  You may
                also provide a simple string containing the DSN URL.
                To make the types() request on multiple servers, pass an
                array reference containing the list of DSNs.

  -segment      (optional) A single segment, or an array ref containing
                several segments.  Segments are either Bio::Das::Segment
                objects, or strings of the form "seq_id:start,end".

  -callback     (optional) Specifies a subroutine to be invoked on each
               stylesheet received.

-dsn, -segment and -callback have the same meaning that they do in similar methods.

@request = $das->get_feature_by_name(-dsn=>[$dsns],-name=>$name [,-class=>$class]);

This method implements the DAS feature request using parameters that will translate a feature name into one or more segments. This can be used to retrieve the section of a genome that is occupied by a particular feature. If the feature name matches multiple features in discontinuous parts of the genome, this call may return multiple segments. Once you have a segment, you can call its features() method to get information about the features that overlap this region.

The optional -class argument is provided to deal with servers that have namespaced their features using a colon. $das->get_feature_by_name(-name=>'foo',-class=>'bar') is exactly equivalent to $das->get_feature_by_name(-name=>'bar:foo').

Because this method is misnamed (it returns segments, not features), it is also known as feature2segment().

In case of a successful request, the request results() method will return a list of Bio::Das::Segment objects, which can then be passed back to features().

Fetching Results

When using the parallel API, the dsn(), features(), dna(), and stylesheet() methods will return an array of Bio::Das::Request objects. Each object contains information about the outcome of the request and the results, if any, returned. The request objects correspond to each of the DSNs passed to the request in the -dsn argument, and have the same number and order.

Because of the inherent uncertainties of the Internet, any DAS request can fail. It could fail because of a network transmission error, a timeout, a down server, an HTTP URL-not-found error, or an unparseable DAS document. For this reason, you should check each request's is_success() method before trying to use the results. Here is the canonical code:

  my @requests = $das->some_method(-dsn=>[$dsn1,$dsn2,$dsn3]);
  for my $request (@requests) {
    if ($request->is_success) {
       my $results = $request->results;
       # do something with the results
    }

    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 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 Bio::Das::Feature objects for the features() request a set of Bio::Das::Stylesheet objects for the stylesheet() request, a set of 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 -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;

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:

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 user and 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);
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.

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

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

The callback will be called with three arguments:

  my_authentication_routine($fetcher,$realm,$iteration_count)

$fetcher is an Bio::Das::HTTP::Fetch object. It contains the information you will need to determine which server is requesting authentication. You will probably want to call the fetch object's host() method to get the name of the DAS host, but if you require more information, the request() method will return the Bio::Das::Request object with complete information about the request.

$realm is the Basic Authentication Realm string, as returned by the remote server.

$iteration_count records the number of times your authentication routine has been invoked for this particular realm. You can use this information to abort authentication if it fails the first time.

The authentication callback should a two-element list containing the username and password for authentication against the server. If it returns an empty list, the request will be aborted.

Here is a sample authentication routine. It prompts the user up to three times for his username and password, and then aborts. Notice the way in which the hostname is recovered from the Bio::Das::HTTP::Fetch object.

 sub my_authentication_routine {
   my ($fetcher,$domain,$iteration_count) = @_;
   return if $iteration_count > 3;
   my $host = $fetcher->request->host;
   print STDERR "$host/$domain requires authentication (try $iteration_count of 3)\n";
   print STDERR "Username: ";
   chomp (my $username = <>);
   print STDERR "Password: ";
   chomp (my $password = <>);
   return ($username,$password);
 }

Note: while processing the authentication callback, processing of other pending requests will stall, usually at the point at which the request has been sent, but the results have not yet been received and parsed. For this reason, you might want to include a timeout in your authentication routine.

AUTHOR ^

Lincoln Stein <lstein@cshl.org>.

Copyright (c) 2001 Cold Spring Harbor Laboratory

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty.

SEE ALSO ^

Bio::Das::Request, Bio::Das::HTTP::Fetch, Bio::Das::Segment, Bio::Das::Type, Bio::Das::Stylesheet, Bio::Das::Source, Bio::RangeI

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