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Bio::DB::EUtilities - Webagent which interacts with and retrieves data from NCBI's eUtils.

Contents

Author

       Chris Fields <cjfields@bioperl.org>

Bio::Db::Genericwebagent Methods

Bio::Tools::Eutilities-Delegating Methods
Bio::Tools::Eutilities::Eutildatai Methods
eutil
        Title    : eutil
        Usage    : $eutil->$foo->eutil
        Function : Get/Set eutil
        Returns  : string
        Args     : string (eutil)
        Throws   : on invalid eutil

   datatype
        Title    : datatype
        Usage    : $type = $foo->datatype;
        Function : Get/Set data object type
        Returns  : string
        Args     : string

   to_string
        Title    : to_string
        Usage    : $foo->to_string()
        Function : converts current object to string
        Returns  : none
        Args     : (optional) simple data for text formatting
        Note     : Implemented in plugins

   print_all
        Title    : print_all
        Usage    : $info->print_all();
                   $info->print_all(-fh => $fh, -cb => $coderef);
        Function : prints (dumps) all data in parser.  Unless a coderef is supplied,
                   this just dumps the parser-specific to_string method to either a
                   file/fh or STDOUT
        Returns  : none
        Args     : [optional]
                  -file : file to print to
                  -fh   : filehandle to print to (cannot be used concurrently with file)
                  -cb   : coderef to use in place of default print method.  This is passed
                          in a LinkSet object
                  -wrap : number of columns to wrap default text output to (def = 80)
        Notes    : only applicable for einfo.  If -file or -fh are not defined,
                   prints to STDOUT


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->method' when needed.

   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)

   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

   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; either eutil name (for returning eutil-specific
                  parameters) or 'history' (for those parameters allowed when retrieving
                  data stored on the remote server using a 'History' object).

   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 passed 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 or 'history', for returning a subset of
                       parameters (Default: returns all)
                  -join_ids : Boolean; join IDs based on correspondence (Default: no join)

   get_parameter_values
        Title   : get_parameter_values
        Usage   : @vals = $factory->get_parameter_value('id'); # always get array
        Function: Returns the specific parameter values.
        Returns : For consistency returns a list of values for this parameter.  If only
                  one is expected, use:

                  ($val) = $factory->get_parameter_value('id');

        Args    : parameter expected


Description
       This is a general webagent which posts and retrieves data to NCBI's eUtils service using their CGI
       interface. A separate project, currently present in BioPerl-Run, utilizes the SOAP-based interface for
       eUtils.

       A full explanation of the eUtils interfaces are not possible within this short module; please see the
       BioPerl wiki HOWTO for more details.


Feedback
Mailinglists
       User feedback is an integral part of the evolution of this and other Bioperl modules. 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.

   Reportingbugs
       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


Genericwebdbi Methods
parameter_base
        Title   : parameter_base
        Usage   : $dbi->parameter_base($pobj);
        Function: Get/Set Bio::ParameterBaseI.
        Returns : Bio::ParameterBaseI object
        Args    : Bio::ParameterBaseI object

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

   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

   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.


Iterator- And Callback-Related Methods
rewind
        Title    : rewind
        Usage    : $esum->rewind()
                   $esum->rewind('recursive')
        Function : retrieve a list of DocSum instances
        Returns  : array of Bio::Tools::EUtilities::Summary::DocSum
        Args     : [optional] Scalar; string ('all') to reset all iterators, or string
                   describing the specific main object iterator to reset. The following
                   are recognized (case-insensitive):

                   'all' - rewind all objects and also recursively resets nested object
                           iterators (such as LinkSets and DocSums).
                   'globalqueries'
                   'fieldinfo' or 'fieldinfos'
                   'linkinfo' or 'linkinfos'
                   'linksets'
                   'docsums'

   generate_iterator
        Title    : generate_iterator
        Usage    : my $coderef = $esum->generate_iterator('linkinfo')
        Function : generates an iterator (code reference) which iterates through
                   the relevant object indicated by the args
        Returns  : code reference
        Args     : [REQUIRED] Scalar; string describing the specific object to iterate.
                   The following are currently recognized (case-insensitive):

                   'globalqueries'
                   'fieldinfo' or 'fieldinfos'
                   'linkinfo' or 'linkinfos'
                   'linksets'
                   'docsums'

                   A second argument can also be passed to generate a 'lazy' iterator,
                   which loops through and returns objects as they are created (instead
                   of creating all data instances up front, then iterating through,
                   which is the default). Use of these iterators precludes use of
                   rewind() for the time being as we can't guarantee you can rewind(),
                   as this depends on whether the data source is seek()able and thus
                   'rewindable'. We will add rewind() support at a later time which
                   will work for 'seekable' data.

                   A callback specified using callback() will be used to filter objects
                   for any generated iterator. This behaviour is implemented for both
                   normal and lazy iterator types and is the default. If you don't want
                   this, make sure to reset any previously set callbacks via
                   reset_callback() (which just deletes the code ref).
        TODO     : generate seekable iterators ala HOP for seekable fh data

   callback
        Title    : callback
        Usage    : $parser->callback(sub {$_[0]->get_database eq 'protein'});
        Function : Get/set callback code ref used to filter returned data objects
        Returns  : code ref if previously set
        Args     : single argument:
                   code ref - evaluates a passed object and returns true or false value
                              (used in iterators)
                   'reset' - string, resets the iterator.
                   returns upon any other args


Methods
Methods Useful For Multiple Eutils
get_ids
        Title    : get_ids
        Usage    : my @ids = $parser->get_ids
        Function : returns array of requested IDs (see Notes for more specifics)
        Returns  : array
        Args     : [conditional] not required except when running elink queries against
                   multiple databases. In case of the latter, the database name is
                   optional but recommended when retrieving IDs as the ID list will
                   be globbed together. In such cases, if a db name isn't provided a
                   warning is issued as a reminder.
        Notes    : esearch    : returned ID list
                   elink      : returned ID list (see Args above for caveats)
                   all others : from parameter_base->id or undef

   get_database
        Title    : get_database
        Usage    : my $db = $info->get_database;
        Function : returns single database name (eutil-compatible).  This is the queried
                   database.  For most eutils this is straightforward.  For elinks
                   (which have 'db' and 'dbfrom') this is dbto, for egquery, it is the first
                   db in the list (you probably want get_databases instead)
        Returns  : string
        Args     : none
        Notes    : egquery    : first db in the query (you probably want get_databases)
                   einfo      : the queried database
                   espell     : the queried database
                   elink      : from parameter_base->dbfrom or undef
                   all others : from parameter_base->db or undef

   get_db(aliasforget_database)get_databases
        Title    : get_databases
        Usage    : my @dbs = $parser->get_databases
        Function : returns list of databases
        Returns  : array of strings
        Args     : none
        Notes    : This is guaranteed to return a list of databases. For a single
                   database use the convenience method get_db/get_database

                   egquery    : list of all databases in the query
                   einfo      : the queried database
                   espell     : the queried database
                   all others : from parameter_base->db or undef

   get_dbs(aliasforget_databases)next_History
        Title    : next_History
        Usage    : while (my $hist=$parser->next_History) {...}
        Function : returns next HistoryI (if present).
        Returns  : Bio::Tools::EUtilities::HistoryI (Cookie or LinkSet)
        Args     : none
        Note     : esearch, epost, and elink are all capable of returning data which
                   indicates search results (in the form of UIDs) is stored on the
                   remote server. Access to this data is wrapped up in simple interface
                   (HistoryI), which is implemented in two classes:
                   Bio::DB::EUtilities::History (the simplest) and
                   Bio::DB::EUtilities::LinkSet. In general, calls to epost and esearch
                   will only return a single HistoryI object (formerly known as a
                   Cookie), but calls to elink can generate many depending on the
                   number of IDs, the correspondence, etc. Hence this iterator, which
                   allows one to retrieve said data one piece at a time.

   next_cookie(aliasfornext_History)get_Histories
        Title    : get_Histories
        Usage    : my @hists = $parser->get_Histories
        Function : returns list of HistoryI objects.
        Returns  : list of Bio::Tools::EUtilities::HistoryI (Cookie or LinkSet)
        Args     : none


Name
       Bio::DB::EUtilities - Webagent which interacts with and retrieves data from NCBI's eUtils.


Synopsis
         my $eutil = Bio::DB::EUtilities->new(
           -eutil      => 'esearch',
           -term       => 'BRCA1',
           -db         => 'pubmed',
           -retmax     => 10000,
           -email      => 'foo@bar.org'); # please use your real email

         # eutil => any of esearch, esummary, elink
         @ids = $eutil->get_ids(); # returns array or array ref of IDs

         # eutil => any of egquery, espell

         $term = $eutil->get_term(); # returns array or array ref of IDs

         # eutil => any of elink, einfo

         $db = $eutil->get_database(); # returns database

         # Query-related methods (esearch, egquery, espell data)
         # eutil data centered on use of search terms

         my $ct = $eutil->get_count; # uses optional database for egquery count
         my $translation = $eutil->get_count;

         my $corrected = $eutil->get_corrected_query; # espell

         while (my $gquery = $eutil->next_GlobalQuery) {
            # iterates through egquery data
         }

         # Info-related methods (einfo data)
         # database-related information

         my $desc = $eutil->get_description;
         my $update = $eutil->get_last_update;
         my $nm = $eutil->get_menu_name;
         my $ct = $eutil->get_record_count;

         while (my $field = $eutil->next_FieldInfo) {
             # ...
         }
         while (my $field = $eutil->next_LinkInfo) {
             # ...
         }

         # History methods (epost data, some data returned from elink)
         # data which enables one to retrieve and query against user-stored
         # information on the NCBI server

         while (my $cookie = $eutil->next_History) {
             # ...
         }

         my @hists = $eutil->get_Histories;

         # Bio::Tools::EUtilities::Summary (esummary data)
         # information on a specific database record

         # retrieve nested docsum data
         while (my $docsum = $eutil->next_DocSum) {
             print "ID:",$docsum->get_ids,"\n";
             while (my $item = $docsum->next_Item) {
                 # do stuff here...
                 while (my $listitem = $docsum->next_ListItem) {
                     # do stuff here...
                     while (my $listitem = $docsum->next_Structure) {
                         # do stuff here...
                     }
                 }
             }
         }

         # retrieve flattened item list per DocSum
         while (my $docsum = $eutil->next_DocSum) {
            my @items = $docsum->get_all_DocSum_Items;
         }


Todo
       •  Finish documentation

          HOWTOs (both standard and Cookbook).

       •  Cookbook tests

          Set up dev-only tests for Cookbook examples to make sure they are consistently updated.

       •  API

          Mark  Jensen has written up the SOAP-based eUtil modules, maybe we should coalesce around a consistent
          API between the two (they are close).

       •  Carryover of parameters

          Maybe add a default but configurable list of parameters that can be carried over between calls.

       •  Make setting certain parameters consistent

          Setting history is a bit inconsistent, so maybe use a common alias for this?

       •  Moosify?

          Not necessary, but it might make things easier and more maintainable in the long run.


Version
       version 1.77


See Also
MCP
Mcp-developer-name  Mcp
Man Pages
LWP::Authen::OAuth2::Args  Man Pages
Man Pages
Usage:  Man Pages
Function
Function  PNG Icons
Title
Title  PNG Icons
Man Pages
Bio::Tools::EUtilities::EUtilDataI  Man Pages
Man Pages
Printing  Man Pages
None
None  PNG Icons
String
String  PNG Icons
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