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Manual Reference Pages  -  BIO::DB::SOAPEUTILITIES::RESULT (3)

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NAME

Bio::DB::SoapEUtilities::Result - Accessor object for SoapEUtilities results

CONTENTS

SYNOPSIS



 $fac = Bio::DB::SoapEUtilities->new();
 $result = $fac->esearch( -db => gene, -term => hedgehog)->run;
 $count = $result->count; # case important; $result->Count could be arrayref
 @ids = $result->ids;



DESCRIPTION

This module attempts to make Entrez Utilities SOAP responses as user-friendly and intuitive as possible. These responses can be complex structures with much useful data; but users will generally desire the values of some key fields. The Result object provides access to all response values via systematically named accessor methods, and commonly used values as convenience methods. The ’raw’ SOAP message (a SOAP::SOM object as returned by SOAP::Lite) is also provided.
Convenience accessors If a list of record ids is returned by the call, ids() will return these as an array reference:



 @seq_ids = $result->ids;



The total count of returned records is provided by count():



 $num_recs = $result->count;



If usehistory was specified in the SOAP call, the NCBI-assigned web environment (that can be used in future calls) is available in webenv, and the query key assigned to the result in query_key:



 $next_result = $fac->efetch( -WebEnv => $result->webenv,
                              -QueryKey => $result->query_key );



Walking the response This module uses AUTOLOAD to provide accessor methods for all response data. Here is an example of a SOAP response as returned by a method() call off the SOAP::SOM object:



    DB<5> x $result->som->method
 0  HASH(0x2eac9a4)
    Count => 148
    IdList => HASH(0x4139578)
      Id => 100136227
    QueryKey => 1
    QueryTranslation => sonic[All Fields] AND hedgehog[All Fields]
    RetMax => 20
    RetStart => 0
    TranslationSet => 
    TranslationStack => HASH(0x4237b4c)
       OP => GROUP
       TermSet => HASH(0x42c43bc)
          Count => 2157
          Explode => Y
          Field => All Fields
          Term => hedgehog[All Fields]
    WebEnv => NCID_1_150423569_130.14.22.101_9001_1262703782



Some of the data values here (at the tips of the data structure) are actually arrays of values ( e.g., the tip IdList = Id> ), other tips are simple scalars. With this in mind, Result accessor methods work as follows:

Data values (at the tips of the response structure) are acquired by calling a method with the structure keys separated by underscores (if necessary):



 $query_key = $result->QueryKey; # $query_key == 1
 $ids = $result->IdList_Id;      # @$ids is an array of record ids



Data sets below a particular node in the response structure can also be obtained with similarly constructed method names. These ’internal node accessors’ return a hashref, containing all data leaves below the node, keyed by the accessor names:



    $data_hash = $result->TranslationStack

    DB<3> x $data_hash
 0  HASH(0x43569d4)
    TranslationStack_OP => ARRAY(0x42d9988)
       0  AND
       1  GROUP
    TranslationStack_TermSet_Count => ARRAY(0x4369c64)
       0  148
       1  148
       2  2157
    TranslationStack_TermSet_Explode => ARRAY(0x4368998)
       0  Y
       1  Y
    TranslationStack_TermSet_Field => ARRAY(0x4368260)
       0  All Fields
       1  All Fields
    TranslationStack_TermSet_Term => ARRAY(0x436c97c)
       0  sonic[All Fields]
       1  hedgehog[All Fields]



Similarly, the call $result-TranslationStack_TermSet > would return a similar hash containing the last 4 elements of the example hash above.

Creating accessors is somewhat costly, especially for fetch responses which can be deep and complex (not unlike BioPerl developers). Portions of the response tree can be ignored by setting -prune_at_node to a arrayref of nodes to skip. Nodes should be specified in SOAP::SOM format, e.g.



 ...::Result->new( -prune_at_nodes => [//GBSeq_references] );



Accessor creation can be skipped altogether by passing -no_parse = 1> to the Result constructor. This is recommended if a result is being passed to a Bio::DB::SoapEUtilities::FetchAdaptor. The original SOAP message with all data is always available in $result-som>.

Other methods

accessors()

An array of available data accessor names. This contains only the data tips. The internal node accessors are autoloaded.

ok()

True if no SOAP fault.

errstr()

Returns the SOAP fault error string.

som()

The original SOAP::SOM message.

util()

The EUtility associated with the result.

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 the Bioperl mailing list. Your participation is much appreciated.



  bioperl-l@bioperl.org                  - General discussion
http://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 of the bugs and their resolution. Bug reports can be submitted via the web:



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



AUTHOR - Mark A. Jensen

Email maj -at- fortinbras -dot- us

APPENDIX

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

parse_methods()



 Title   : parse_methods
 Usage   :
 Function: parse out the accessor methods
 Returns : self (Result object)
 Args    : $alias_hash (hashref), $prune_at_nodes (scalar or arrayref)



util()



 Title   : util
 Usage   :
 Function: Name of the utility producing this result object.
 Returns : scalar string
 Args    :



som()



 Title   : som
 Usage   :
 Function: get the original SOAP::SOM object
 Returns : a SOAP::SOM object
 Args    : none



ok()



 Title   : ok
 Usage   :
 Function:
 Returns : true if no SOAP fault
 Args    :



errstr()



 Title   : errstr
 Usage   :
 Function:
 Returns : fault string of SOAP object
 Args    : none



accessors()



 Title   : accessors
 Usage   :
 Function: get the list of created accessors for this
           result
 Returns : array of scalar strings
 Args    : none
 Note    : does not include valid AUTOLOADed accessors; see
           DESCRIPTION



webenv()



 Title   : webenv
 Usage   :
 Function: contains WebEnv key referencing this
           results session
 Returns : scalar
 Args    : none



query_key()()



 Title   : query_key()
 Usage   :
 Function: contains the web query key assigned
           to this result
 Returns : scalar
 Args    :



fetch_type()



 Title   : fetch_type
 Usage   :
 Function: Get the efetch database name according to WSDL
 Returns : scalar string (db name) or undef if N/A
 Args    : none



POD ERRORS

Hey! <B>The above document had some coding errors, which are explained below:B>
Around line 137: You can’t have =items (as at line 141) unless the first thing after the =over is an =item
Search for    or go to Top of page |  Section 3 |  Main Index


perl v5.20.3 BIO::DB::SOAPEUTILITIES::RESULT (3) 2016-04-05

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