Christopher Fields > BioPerl-1.6.901 > Bio::DB::EUtilities

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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;
  }

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.

TODO ^

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.

  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::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.

LWP::UserAgent related methods ^

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

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

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.

next_cookie (alias for next_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

Query-related methods ^

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_terms
 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

print_GlobalQueries

 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

Summary-related methods ^

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

print_DocSums

 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

Info-related methods ^

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.  

print_FieldInfo

 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

print_LinkInfo

 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

Bio::Tools::EUtilities::Link-related methods ^

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.  

print_LinkSets

 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.

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
                    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
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