Bio::T...ameters(3pm)

💖 Bio::Tools::EUtilities::EUtilParameters 💖

okay bestie, welcome to the manual page for Bio::Tools::EUtilities::EUtilParameters (that's the Bio::T...ameters(3pm) one, yeah, they abbreviate it in the header, we're not gonna do that here). It's the module that handles manipulation of NCBI eutil-based parameters for remote database requests. Lowkey iconic, fr fr. ✨

🌸 VERSION 🌸

version 1.77

🎀 SYNOPSIS 🎀

# Bio::Tools::EUtilities::EUtilParameters implements Bio::ParameterBaseI

my @params = (-eutil => 'efetch',
             db => 'nucleotide',
             id => \@ids,
             api_key => 'mYApiKeyFrOMNCBI',
             email => 'me@foo.bar',
             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 🦋

So Bio::Tools::EUtilities::EUtilParameters is-a Bio::ParameterBaseI implementation, and what it does is let you do simple manipulation of NCBI eutil parameters for CGI-based queries. SOAP-based methods may be added in the future (they're not here yet, don't come for me).

The way this works, for simplicity: parameters do not require dashes when you pass them, and they do not need URI encoding — spaces get converted to '+', symbols get encoded, etc. It just handles it. 💅

Also, these 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).

ngl, at this point minimal checking is done for potential errors in parameter passing, though these should be easily added in the future when necessary. So like, be a little mindful. 🙈

---

✨ 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 api_key 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)

Status: NYI — it's giving "not yet implemented", bestie. 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'
                   supersedes 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::https 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?

🔥 heads up: calling to_request changes state of object (to boolean FALSE). It's for CGI-based GET/POST, so don't be surprised bestie.

---

🧚 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

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🫶 FEEDBACK 🫶

💌 Mailing lists

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

bioperl-l@bioperl.org               - General discussion
https://bioperl.org/Support.html    - About the mailing lists

💌 Support

Please direct usage questions or support issues to the mailing list: bioperl-l@bioperl.org 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. (yes it says "reponsive" in the original, we're keeping it, it's iconic in its own way 🫶)

💌 Reporting bugs

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

https://github.com/bioperl/bio-eutilities/issues

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🌟 AUTHOR 🌟

Chris Fields <cjfields@bioperl.org>

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💖 COPYRIGHT 💖

Okay bestie, legal era, let's get into it. ✨

This software is copyright (c) 2006-2013 by Chris Fields. 👑

This software is available under the same terms as the perl 5 programming language system itself. 🐪 slay

tl;dr: same license vibes as perl itself, no cap. Read it, love it, respect the terms. 💅

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And that's a wrap on the whole page, bestie!! 🎀 You made it to the very end, which is honestly main character behavior. 🦋 This one came to you from perl v5.40.0, dated 2025-01-27, and it lives in the User Contributed Perl Documentation corner of the internet. 🌸 Go forth and parameterize responsibly. Mwah. 💋✨