Bio-EUtilities

 view release on metacpan or  search on metacpan

lib/Bio/DB/EUtilities.pm  view on Meta::CPAN

 Returns : Bio::ParameterBaseI object
 Args    : Bio::ParameterBaseI object

=head2 ua

 Title   : ua
 Usage   : $dbi->ua;
 Function: Get/Set LWP::UserAgent.
 Returns : LWP::UserAgent
 Args    : LWP::UserAgent

=head2 get_Response

 Title   : get_Response
 Usage   : $agent->get_Response;
 Function: Get the HTTP::Response object by passing it an HTTP::Request (generated from
           Bio::ParameterBaseI implementation).
 Returns : HTTP::Response object or data if callback is used
 Args    : (optional)

           -cache_response - flag to cache HTTP::Response object;
                             Default is 1 (TRUE, caching ON)

           These are passed on to LWP::UserAgent::request() if stipulated

           -cb     - use a LWP::UserAgent-compliant callback
           -file   - dumps the response to a file (handy for large responses)
                     Note: can't use file and callback at the same time
           -read_size_hint - bytes of content to read in at a time to pass to callback
 Note    : Caching and parameter checking are set

=head2 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.

=head1 LWP::UserAgent related methods

=head2 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)

=head2 authentication

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

=head2 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: NCBI requests a delay of 3 requests per second. This method implements
  that policy. This will likely change to check time of day or number of
  requests for lengthening delays.

=head2 get_Parser

 Title   : get_Parser
 Usage   : $agent->get_Parser;
 Function: Retrieve the parser used for last agent request
 Returns : The Bio::Tools::EUtilities parser used to parse the HTTP::Response
           content
 Args    : None
 Note    : Abstract method; defined by implementation

=head1 Bio::Tools::EUtilities::EUtilParameters-delegating methods

This is only a subset of parameters available from Bio::Tools::EUtilities::EUtilParameters (the
ones deemed absolutely necessary).  All others are available by calling
'parameter_base-E<gt>method' when needed.

=head2 set_parameters

 Title   : set_parameters
 Usage   : $pobj->set_parameters(@params);
 Function: sets the NCBI parameters listed in the hash or array
 Returns : None
 Args    : [optional] hash or array of parameter/values.
 Note    : This sets any parameter (i.e. doesn't screen them).  In addition to
           regular eutil-specific parameters, you can set the following:

           -eutil    - the eUtil to be used (default 'efetch')
           -history  - pass a HistoryI-implementing object, which
                       sets the WebEnv, query_key, and possibly db and linkname
                       (the latter two only for LinkSets)
           -correspondence - Boolean flag, set to TRUE or FALSE; indicates how
                       IDs are to be added together for elink request where
                       ID correspondence might be needed
                       (default 0)

=head2 reset_parameters

 Title   : reset_parameters
 Usage   : resets values
 Function: resets parameters to either undef or value in passed hash
 Returns : none
 Args    : [optional] hash of parameter-value pairs
 Note    : this also resets eutil(), correspondence(), and the history and request
           cache



( run in 0.901 second using v1.01-cache-2.11-cpan-cdf2f3d4e48 )