Reference

Bio::DB::GenericWebDBI(3pm)

Bio::DB::GenericWebDBI - abstract interface for parameter-based remote database access

  #
  # grab data from HTTP::Response object using concrete class
  #


  $data = $db->get_response->content;


  #
  # $data is the raw data output from the HTTP::Response object;
  # this data may be preparsed using the private method _parse_response

WARNING: Please do NOT spam the web servers with multiple requests. This class acts as a user agent interface for any generic web database, but is specifically geared towards CGI-based databases which accept parameters. File and filehandle support to be added Any feedback is welcome.
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Email cjfields at uiuc dot edu The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
url_base_address

 Title   : url_base_address
 Usage   : my $address = $self->url_base_address or
           $self->url_base_address($address)
 Function: Get/Set the base URL for the Web Database
 Returns : Base URL for the Web Database
 Args    : $address - URL for the WebDatabase

proxy

 Title   : proxy
 Usage   : $httpproxy = $db->proxy('http')  or
           $db->proxy(['http','ftp'], 'http://myproxy' )
 Function: Get/Set a proxy for use of proxy
 Returns : a string indicating the proxy
 Args    : $protocol : an array ref of the protocol(s) to set/get
           $proxyurl : url of the proxy to use for the specified protocol
           $username : username (if proxy requires authentication)
           $password : password (if proxy requires authentication)

authentication

 Title   : authentication
 Usage   : $db->authentication($user,$pass)
 Function: Get/Set authentication credentials
 Returns : Array of user/pass
 Args    : Array or user/pass

db

 Title   : db
 Usage   : $db->db
 Function: Get/Set database parameter
 Returns : string
 Args    : optional string

id

 Title   : id
 Usage   : $agent->id($id)
           $agent->id(\@id)
 Function: Get/Set id(s)
 Returns : reference to id(s)
 Args    : a single id or reference to array of id(s)

retmode

 Title   : retmode
 Usage   : $agent->retmode($mode)
 Function: Get/Set return mode for query (text, xml, html, asn.1, etc)
 Returns : string for return mode
 Args    : optional string

get_response

 Title   : get_response
 Usage   : $agent->get_response;
 Function: get the request based on set object parameters, retrieved using
           the private method _get_params
 Returns : HTTP::Response object
 Args    : none


 This is implemented by the derived class

delay

 Title   : delay
 Usage   : $secs = $self->delay([$secs])
 Function: get/set number of seconds to delay between fetches
 Returns : number of seconds to delay
 Args    : new value

NOTE: the default is to use the value specified by delay_policy(). This can be overridden by calling this method, or by passing the -delay argument to new().
delay_policy

 Title   : delay_policy
 Usage   : $secs = $self->delay_policy
 Function: return number of seconds to delay between calls to remote db
 Returns : number of seconds to delay
 Args    : none

NOTE: The default delay policy is 0s. Override in subclasses to implement delays. The timer has only second resolution, so the delay will actually be +/- 1s.
_submit_request

  Title   : _submit_request
  Usage   : my $url = $self->get_request
  Function: builds request object based on set parameters
  Returns : HTTP::Request
  Args    : optional : Bio::DB::EUtilities cookie

_get_params

  Title   : _get_params
  Usage   : my $url = $self->_get_params
  Function: builds parameter list for web request
  Returns : hash of parameter-value paris
  Args    : optional : Bio::DB::EUtilities cookie

_sleep

 Title   : _sleep
 Usage   : $self->_sleep
 Function: sleep for a number of seconds indicated by the delay policy
 Returns : none
 Args    : none

NOTE: This method keeps track of the last time it was called and only imposes a sleep if it was called more recently than the delay_policy() allows.