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Bio::DB::GenericWebDBI.3pm
Langue: en
Version: 2008-01-11 (mandriva - 01/05/08)
Section: 3 (Bibliothèques de fonctions)
NAME
Bio::DB::GenericWebDBI - abstract interface for parameter-based remote database accessSYNOPSIS
# # 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 addedAny 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 eduAPPENDIX
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.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre