Provided by: libbio-perl-run-perl_1.6.9-3_all 
NAME
Bio::DB::SoapEUtilities::Result - Accessor object for SoapEUtilities results
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
result's 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! The above document had some coding errors, which are explained below:
Around line 137:
You can't have =items (as at line 141) unless the first thing after the =over is an =item