SYNOPSIS

# Bio::Tools::EUtilities::EUtilParameters implements Bio::ParameterBaseI
my @params = (-eutil => 'efetch',
db => 'nucleotide',
id => \@ids,
email => '[email protected]',
retmode => 'xml');
my $p = Bio::Tools::EUtilities::EUtilParameters->new(@params);
if ($p->parameters_changed) {
# ...
} # state information
$p->set_parameters(@extra_params); # set new NCBI parameters, leaves others preset
$p->reset_parameters(@new_params); # reset NCBI parameters to original state
$p->to_string(); # get a URI-encoded string representation of the URL address
$p->to_request(); # get an HTTP::Request object (to pass on to LWP::UserAgent)

DESCRIPTION

Bio::Tools::EUtilities::EUtilParameters is-a Bio::ParameterBaseI implementation that allows simple manipulation of NCBI eutil parameters for CGI-based queries. SOAP-based methods may be added in the future.

For simplicity parameters do not require dashes when passed and do not need URI encoding (spaces are converted to '+', symbols encoded, etc). Also, the following extra parameters can be passed to the new() constructor or via set_parameters() or reset_parameters():

  eutil - the eutil to be used. The default is 'efetch' if not set.
  correspondence - Flag for how IDs are treated. Default is undef (none).
  history - a Bio::Tools::EUtilities::HistoryI object. Default is undef (none).

At this point minimal checking is done for potential errors in parameter passing, though these should be easily added in the future when necessary.

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.

  [email protected]               - General discussion
  http://www.bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

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.

  https://redmine.open-bio.org/projects/bioperl/

AUTHOR

Email cjfields at bioperl dot org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

Bio::ParameterBaseI implemented methods

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 passed but leaves previously set data alone.
           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)

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 sets any parameter passed, but resets all others (deletes 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)

carryover

 Title    : carryover
 Usage    : $obj->carryover(qw(email tool db))
 Function : Carries over the designated parameters when using reset_parameters()
 Returns  : a list of carried-over parameters
 Args     : An array reference of parameters to carry over, followed optionally
            by the mode ('add' or 'delete', indicating whether to append to or
            remove the specified values passed in). To clear all values, pass in
            an empty array reference (the mode in this case doesn't matter).
            
            In addition to the normal eUtil-specific parameters, the following
            additional parameters are allowed:
            
            -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)
 Default  : None (no carried over parameters)
 Status   : NYI (dev in progress, carry on, nothing to see here)

request_mode

 Title    : request_mode
 Usage    : $obj->request_mode
 Function : get/set the mode for the user agent to use for generating a request
 Returns  : either a preset mode (checked against the eutil) or a best-possible
            option based upon the currently-set parameters
 Args     : 
 Status   :

parameters_changed

 Title   : parameters_changed
 Usage   : if ($pobj->parameters_changed) {...}
 Function: Returns TRUE if parameters have changed
 Returns : Boolean (0 or 1)
 Args    : [optional] Boolean

available_parameters

 Title   : available_parameters
 Usage   : @params = $pobj->available_parameters()
 Function: Returns a list of the available parameters
 Returns : Array of available parameters (no values)
 Args    : [optional] A string with the eutil name (for returning eutil-specific
           parameters)

get_parameters

 Title   : get_parameters
 Usage   : @params = $pobj->get_parameters;
           %params = $pobj->get_parameters;
 Function: Returns list of key/value pairs, parameter => value
 Returns : Flattened list of key-value pairs. All key-value pairs returned,
           though subsets can be returned based on the '-type' parameter. Data
           originally set as an array ref are returned based on whether the
           '-join_id' flag is set (default is the same array ref).
 Args    : -type : the eutil name (Default: returns all).  Use of '-list'
                    supercedes this
           -list : array ref of specific parameters
           -join_ids : Boolean; join IDs based on correspondence (Default: no join)

Implementation-specific to_* methods

to_string

 Title   : to_string
 Usage   : $string = $pobj->to_string;
 Function: Returns string (URL only in this case)
 Returns : String (URL only for now)
 Args    : [optional] 'all'; build URI::http using all parameters
           Default : Builds based on allowed parameters (presence of history data
           or eutil type in %MODE).
 Note    : Changes state of object.  Absolute string

to_request

 Title   : to_request
 Usage   : $uri = $pobj->to_request;
 Function: Returns HTTP::Request object
 Returns : HTTP::Request
 Args    : [optional] 'all'; builds request using all parameters
           Default : Builds based on allowed parameters (presence of history data
           or eutil type in %MODE).
 Note    : Changes state of object (to boolean FALSE).  Used for CGI-based GET/POST
 TODO    : esearch, esummary, elink now accept POST for batch submission
           (something NCBI apparently allowed but didn't advertise). Should we
           switch most of these to utilize POST instead, or make it dep on the
           number of submitted IDs?

Implementation specific-methods

eutil

 Title   : eutil
 Usage   : $p->eutil('efetch')
 Function: gets/sets the eutil for this set of parameters
 Returns : string (eutil)
 Args    : [optional] string (eutil)
 Throws  : '$eutil not supported' if eutil not present
 Note    : This does not reset retmode to the default if called directly.

history

 Title   : history
 Usage   : $p->history($history);
 Function: gets/sets the history object to be used for these parameters
 Returns : Bio::Tools::EUtilities::HistoryI (if set)
 Args    : [optional] Bio::Tools::EUtilities::HistoryI 
 Throws  : Passed something other than a Bio::Tools::EUtilities::HistoryI 
 Note    : This overrides WebEnv() and query_key() settings when set.  This
           caches the last history object passed and returns like a Get/Set

correspondence

 Title   : correspondence
 Usage   : $p->correspondence(1);
 Function: Sets flag for posting IDs for one-to-one correspondence
 Returns : Boolean
 Args    : [optional] boolean value

id_file

 Title   : id_file
 Usage   : $p->id_file('<foo');
 Function: convenience method; passes in file containing a list of IDs for
           searches (one per line), sets id() to list
 Returns : none
 Args    : either string indicating file to use, a file handle, or an IO::Handle
           object
 Note    : use of this overrides concurrent use of the '-id' parameter when both
           are passed.  The filename is not retained, merely parsed for IDs.

url_base_address

 Title   : url_base_address
 Usage   : $address = $p->url_base_address();
 Function: Get URL base address
 Returns : String
 Args    : None in this implementation; the URL is fixed

set_default_retmode

 Title   : set_default_retmode
 Usage   : $p->set_default_retmode();
 Function: sets retmode to default value specified by the eutil() and the value
           in %NCBI_DATABASE (for efetch only) if called
 Returns : none
 Args    : none