/ 
bioperl-1.5.2_004-RCd
/ Bio::DB::GenericWebDBI

NAME

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

SYNOPSIS

#
# 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

DESCRIPTION

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.

TODO

File and filehandle support to be added

Any feedback is welcome.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

bioperl-l@lists.open-bio.org               - General discussion
http://www.bioperl.org/wiki/Mailing_lists  - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web.

http://bugzilla.open-bio.org/

AUTHOR

Email cjfields at uiuc dot edu

APPENDIX

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.