Bio::DB::EUtilities.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

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

SYNOPSIS

   # ...To be added!
 
 

DESCRIPTION

This is a general webagent which posts and retrieves data to NCBI's eUtilities service using their CGI interface.

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
 
 

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.

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 bioperl dot org

APPENDIX

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

Bio::DB::GenericWebAgent methods

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.

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
 
 

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.
 
 

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
 
 

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
 
 

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
 
 
  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
 
 

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 (alias for get_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 (alias for get_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.
 
 

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
 
 

get_count

  Title    : get_count
  Usage    : my $ct = $parser->get_count
  Function : returns the count (hits for a search)
  Returns  : integer
  Args     : [CONDITIONAL] string with database name - used to retrieve
             count from specific database when using egquery
  Notes    : egquery    : count for specified database (specified above)
             esearch    : count for last search
             all others : undef
 
 

get_term

  Title    : get_term
  Usage    : $st = $qd->get_term;
  Function : retrieve the term for the global search
  Returns  : string
  Args     : none
  Notes    : egquery    : search term
             espell     : search term
             esearch    : from parameter_base->term or undef
             all others : undef
 
 

get_translation_from

  Title   : get_translation_from
  Usage   : $string = $qd->get_translation_from();
  Function: portion of the original query replaced with translated_to()
  Returns : string
  Args    : none
  Note    : only applicable for esearch
 
 

get_translation_to

  Title   : get_translation_to
  Usage   : $string = $qd->get_translation_to();
  Function: replaced string used in place of the original query term in translation_from()
  Returns : string
  Args    : none
  Note    : only applicable for esearch
 
 

get_retstart

  Title    : get_retstart
  Usage    : $start = $qd->get_retstart();
  Function : retstart setting for the query (either set or NCBI default)
  Returns  : Integer
  Args     : none
  Notes    : esearch    : retstart
             esummary   : retstart
             all others : from parameter_base->retstart or undef
 
 

get_retmax

  Title    : get_retmax
  Usage    : $max = $qd->get_retmax();
  Function : retmax setting for the query (either set or NCBI default)
  Returns  : Integer
  Args     : none
  Notes    : esearch    : retmax
             esummary   : retmax
             all others : from parameter_base->retmax or undef
 
 

get_query_translation

  Title   : get_query_translation
  Usage   : $string = $qd->get_query_translation();
  Function: returns the translated query used for the search (if any)
  Returns : string
  Args    : none
  Notes   : only applicable for esearch.  This is the actual term used for
            esearch.
 
 

get_corrected_query

  Title    : get_corrected_query
  Usage    : my $cor = $eutil->get_corrected_query;
  Function : retrieves the corrected query when using espell
  Returns  : string
  Args     : none
  Notes    : only applicable for espell.
 
 

get_replaced_terms

  Title    : get_replaced_terms
  Usage    : my $term = $eutil->get_replaced_term
  Function : returns array of strings replaced in the query
  Returns  : string 
  Args     : none
  Notes    : only applicable for espell
 
 

next_GlobalQuery

  Title    : next_GlobalQuery
  Usage    : while (my $query = $eutil->next_GlobalQuery) {...}
  Function : iterates through the queries returned from an egquery search
  Returns  : GlobalQuery object
  Args     : none
  Notes    : only applicable for egquery
 
 

get_GlobalQueries

  Title    : get_GlobalQueries
  Usage    : @queries = $eutil->get_GlobalQueries
  Function : returns list of GlobalQuery objects
  Returns  : array of GlobalQuery objects
  Args     : none
  Notes    : only applicable for egquery
 
 
  Title    : print_GlobalQueries
  Usage    : $docsum->print_GlobalQueries();
             $docsum->print_GlobalQueries(-fh => $fh, -cb => $coderef);
  Function : prints item data for all global queries.  The default printing
             method is each item per DocSum is printed with relevant values if
             present in a simple table using Text::Wrap. 
  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 GlobalQuery object;
            -wrap : number of columns to wrap default text output to (def = 80)
  Notes    : only applicable for esummary.  If -file or -fh are not defined,
             prints to STDOUT
 
 

next_DocSum

  Title    : next_DocSum
  Usage    : while (my $ds = $esum->next_DocSum) {...}
  Function : iterate through DocSum instances
  Returns  : single Bio::Tools::EUtilities::Summary::DocSum
  Args     : none yet
  Notes    : only applicable for esummary
 
 

get_DocSums

  Title    : get_DocSums
  Usage    : my @docsums = $esum->get_DocSums
  Function : retrieve a list of DocSum instances
  Returns  : array of Bio::Tools::EUtilities::Summary::DocSum
  Args     : none
  Notes    : only applicable for esummary
 
 
  Title    : print_DocSums
  Usage    : $docsum->print_DocSums();
             $docsum->print_DocSums(-fh => $fh, -cb => $coderef);
  Function : prints item data for all docsums.  The default printing method is
             each item per DocSum is printed with relevant values if present
             in a simple table using Text::Wrap.  
  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 DocSum object;
            -wrap : number of columns to wrap default text output to (def = 80)
  Notes    : only applicable for esummary.  If -file or -fh are not defined,
             prints to STDOUT
 
 

get_available_databases

  Title    : get_available_databases
  Usage    : my @dbs = $info->get_available_databases
  Function : returns list of available eutil-compatible database names
  Returns  : Array of strings 
  Args     : none
  Notes    : only applicable for einfo.
 
 

get_record_count

  Title    : get_record_count
  Usage    : my $ct = $eutil->get_record_count;
  Function : returns database record count
  Returns  : integer
  Args     : none
  Notes    : only applicable for einfo.
 
 

get_last_update

  Title    : get_last_update
  Usage    : my $time = $info->get_last_update;
  Function : returns string containing time/date stamp for last database update
  Returns  : integer
  Args     : none
  Notes    : only applicable for einfo.
 
 

get_menu_name

  Title    : get_menu_name
  Usage    : my $nm = $info->get_menu_name;
  Function : returns string of database menu name
  Returns  : string
  Args     : none
  Notes    : only applicable for einfo.
 
 

get_description

  Title    : get_description
  Usage    : my $desc = $info->get_description;
  Function : returns database description
  Returns  : string
  Args     : none
  Notes    : only applicable for einfo.
 
 

next_FieldInfo

  Title    : next_FieldInfo
  Usage    : while (my $field = $info->next_FieldInfo) {...}
  Function : iterate through FieldInfo objects
  Returns  : Field object
  Args     : none
  Notes    : only applicable for einfo. Uses callback() for filtering if defined
             for 'fields'
 
 

get_FieldInfo

  Title    : get_FieldInfo
  Usage    : my @fields = $info->get_FieldInfo;
  Function : returns list of FieldInfo objects
  Returns  : array (FieldInfo objects)
  Args     : none
  Notes    : only applicable for einfo.
 
 

next_LinkInfo

  Title    : next_LinkInfo
  Usage    : while (my $link = $info->next_LinkInfo) {...}
  Function : iterate through LinkInfo objects
  Returns  : LinkInfo object
  Args     : none
  Notes    : only applicable for einfo.  Uses callback() for filtering if defined
             for 'linkinfo'
 
 

get_LinkInfo

  Title    : get_LinkInfo
  Usage    : my @links = $info->get_LinkInfo;
  Function : returns list of LinkInfo objects
  Returns  : array (LinkInfo objects)
  Args     : none
  Notes    : only applicable for einfo.
 
 
  Title    : print_FieldInfo
  Usage    : $info->print_FieldInfo();
             $info->print_FieldInfo(-fh => $fh, -cb => $coderef);
  Function : prints field data for each FieldInfo object. The default method
             prints data from each FieldInfo in a simple table using Text::Wrap.  
  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.  
            -wrap : number of columns to wrap default text output to (def = 80)
  Note     : if -file or -fh are not defined, prints to STDOUT
 
 
  Title    : print_LinkInfo
  Usage    : $info->print_LinkInfo();
             $info->print_LinkInfo(-fh => $fh, -cb => $coderef);
  Function : prints link data for each LinkInfo object. The default is generated
             via LinkInfo::to_string
  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 LinkInfo 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
 
 

next_LinkSet

  Title    : next_LinkSet
  Usage    : while (my $ls = $eutil->next_LinkSet {...}
  Function : iterate through LinkSet objects
  Returns  : LinkSet object
  Args     : none
  Notes    : only applicable for elink.  Uses callback() for filtering if defined
             for 'linksets'
 
 

get_LinkSets

  Title    : get_LinkSets
  Usage    : my @links = $info->get_LinkSets;
  Function : returns list of LinkSets objects
  Returns  : array (LinkSet objects)
  Args     : none
  Notes    : only applicable for elink.
 
 
  Title    : print_LinkSets
  Usage    : $info->print_LinkSets();
             $info->print_LinkSets(-fh => $fh, -cb => $coderef);
  Function : prints link data for each LinkSet object. The default is generated
             via LinkSet::to_string
  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
 
 

get_linked_databases

  Title    : get_linked_databases
  Usage    : my @dbs = $eutil->get_linked_databases
  Function : returns list of databases linked to in linksets
  Returns  : array of databases
  Args     : none
  Notes    : only applicable for elink.
 
 

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
                     interators (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