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.\"
.IX Title "Bio::DB::SoapEUtilities::Result 3pm"
.TH Bio::DB::SoapEUtilities::Result 3pm "2023-01-22" "perl v5.36.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.if n .ad l
.nh
.SH "NAME"
Bio::DB::SoapEUtilities::Result \- Accessor object for SoapEUtilities results
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 4
\& $fac = Bio::DB::SoapEUtilities\->new();
\& $result = $fac\->esearch( \-db => \*(Aqgene\*(Aq, \-term => \*(Aqhedgehog\*(Aq)\->run;
\& $count = $result\->count; # case important; $result\->Count could be arrayref
\& @ids = $result\->ids;
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This module attempts to make Entrez Utilities \s-1SOAP\s0 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'
\&\s-1SOAP\s0 message (a \s-1SOAP::SOM\s0 object as returned by SOAP::Lite) is
also provided.
.IP "Convenience accessors" 4
.IX Item "Convenience accessors"
If a list of record ids is returned by the call, \f(CW\*(C`ids()\*(C'\fR will return these as
an array reference:
.Sp
.Vb 1
\& @seq_ids = $result\->ids;
.Ve
.Sp
The total count of returned records is provided by \f(CW\*(C`count()\*(C'\fR:
.Sp
.Vb 1
\& $num_recs = $result\->count;
.Ve
.Sp
If \f(CW\*(C`usehistory\*(C'\fR was specified in the \s-1SOAP\s0 call, the NCBI-assigned web
environment (that can be used in future calls) is available in
\&\f(CW\*(C`webenv\*(C'\fR, and the query key assigned to the result in \f(CW\*(C`query_key\*(C'\fR:
.Sp
.Vb 2
\& $next_result = $fac\->efetch( \-WebEnv => $result\->webenv, 
\&                              \-QueryKey => $result\->query_key );
.Ve
.IP "Walking the response" 4
.IX Item "Walking the response"
This module uses \f(CW\*(C`AUTOLOAD\*(C'\fR to provide accessor methods for all response data.
Here is an example of a \s-1SOAP\s0 response as returned by a \f(CW\*(C`method()\*(C'\fR call off the \s-1SOAP::SOM\s0 object:
.Sp
.Vb 10
\&    DB<5> x $result\->som\->method
\& 0  HASH(0x2eac9a4)
\&    \*(AqCount\*(Aq => 148
\&    \*(AqIdList\*(Aq => HASH(0x4139578)
\&      \*(AqId\*(Aq => 100136227
\&    \*(AqQueryKey\*(Aq => 1
\&    \*(AqQueryTranslation\*(Aq => \*(Aqsonic[All Fields] AND hedgehog[All Fields]\*(Aq
\&    \*(AqRetMax\*(Aq => 20
\&    \*(AqRetStart\*(Aq => 0
\&    \*(AqTranslationSet\*(Aq => \*(Aq\*(Aq
\&    \*(AqTranslationStack\*(Aq => HASH(0x4237b4c)
\&       \*(AqOP\*(Aq => \*(AqGROUP\*(Aq
\&       \*(AqTermSet\*(Aq => HASH(0x42c43bc)
\&          \*(AqCount\*(Aq => 2157
\&          \*(AqExplode\*(Aq => \*(AqY\*(Aq
\&          \*(AqField\*(Aq => \*(AqAll Fields\*(Aq
\&          \*(AqTerm\*(Aq => \*(Aqhedgehog[All Fields]\*(Aq
\&    \*(AqWebEnv\*(Aq => \*(AqNCID_1_150423569_130.14.22.101_9001_1262703782\*(Aq
.Ve
.Sp
Some of the data values here (at the tips of the data structure) are
actually arrays of values ( e.g., the tip \f(CW\*(C`IdList =\*(C'\fR Id> ), other
tips are simple scalars. With this in mind, \f(CW\*(C`Result\*(C'\fR accessor methods work as
follows:
.Sp
Data values (at the tips of the response structure) are acquired by calling a method with the structure keys separated by underscores (if necessary):
.Sp
.Vb 2
\& $query_key = $result\->QueryKey; # $query_key == 1
\& $ids = $result\->IdList_Id;      # @$ids is an array of record ids
.Ve
.Sp
Data \fIsets\fR 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:
.Sp
.Vb 1
\&    $data_hash = $result\->TranslationStack
\& 
\&    DB<3> x $data_hash
\& 0  HASH(0x43569d4)
\&    \*(AqTranslationStack_OP\*(Aq => ARRAY(0x42d9988)
\&       0  \*(AqAND\*(Aq
\&       1  \*(AqGROUP\*(Aq
\&    \*(AqTranslationStack_TermSet_Count\*(Aq => ARRAY(0x4369c64)
\&       0  148
\&       1  148
\&       2  2157
\&    \*(AqTranslationStack_TermSet_Explode\*(Aq => ARRAY(0x4368998)
\&       0  \*(AqY\*(Aq
\&       1  \*(AqY\*(Aq
\&    \*(AqTranslationStack_TermSet_Field\*(Aq => ARRAY(0x4368260)
\&       0  \*(AqAll Fields\*(Aq
\&       1  \*(AqAll Fields\*(Aq
\&    \*(AqTranslationStack_TermSet_Term\*(Aq => ARRAY(0x436c97c)
\&       0  \*(Aqsonic[All Fields]\*(Aq
\&       1  \*(Aqhedgehog[All Fields]\*(Aq
.Ve
.Sp
Similarly, the call \f(CW\*(C` $result\-\*(C'\fRTranslationStack_TermSet > would
return a similar hash containing the last 4 elements of the example
hash above.
.Sp
Creating accessors is somewhat costly, especially for fetch responses
which can be deep and complex (not unlike BioPerl
developers). Portions of the response tree can be ignored by setting
\&\f(CW\*(C`\-prune_at_node\*(C'\fR to a arrayref of nodes to skip. Nodes should be
specified in \s-1SOAP::SOM\s0 format, e.g.
.Sp
.Vb 1
\& ...::Result\->new( \-prune_at_nodes => [\*(Aq//GBSeq_references\*(Aq] );
.Ve
.Sp
Accessor creation can be skipped altogether by passing \f(CW\*(C`\-no_parse =\*(C'\fR
1> to the \f(CW\*(C`Result\*(C'\fR constructor. This is recommended if a result is
being passed to a
Bio::DB::SoapEUtilities::FetchAdaptor. The original \s-1SOAP\s0
message with all data is always available in \f(CW\*(C`$result\-\*(C'\fRsom>.
.PP
Other methods
.IP "\fBaccessors()\fR" 4
.IX Item "accessors()"
An array of available data accessor names. This
contains only the data \*(L"tips\*(R". The internal node accessors are
autoloaded.
.IP "\fBok()\fR" 4
.IX Item "ok()"
True if no \s-1SOAP\s0 fault.
.IP "\fBerrstr()\fR" 4
.IX Item "errstr()"
Returns the \s-1SOAP\s0 fault error string.
.IP "\fBsom()\fR" 4
.IX Item "som()"
The original \f(CW\*(C`SOAP::SOM\*(C'\fR message.
.IP "\fButil()\fR" 4
.IX Item "util()"
The EUtility associated with the result.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
bioperl\-l@bioperl.org
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  http://redmine.open\-bio.org/projects/bioperl/
.Ve
.SH "AUTHOR \- Mark A. Jensen"
.IX Header "AUTHOR - Mark A. Jensen"
Email maj \-at\- fortinbras \-dot\- us
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "\fBparse_methods()\fP"
.IX Subsection "parse_methods()"
.Vb 5
\& Title   : parse_methods
\& Usage   : 
\& Function: parse out the accessor methods
\& Returns : self (Result object)
\& Args    : $alias_hash (hashref), $prune_at_nodes (scalar or arrayref)
.Ve
.SS "\fButil()\fP"
.IX Subsection "util()"
.Vb 5
\& Title   : util
\& Usage   : 
\& Function: Name of the utility producing this result object.
\& Returns : scalar string
\& Args    :
.Ve
.SS "\fBsom()\fP"
.IX Subsection "som()"
.Vb 5
\& Title   : som
\& Usage   : 
\& Function: get the original SOAP::SOM object
\& Returns : a SOAP::SOM object
\& Args    : none
.Ve
.SS "\fBok()\fP"
.IX Subsection "ok()"
.Vb 5
\& Title   : ok
\& Usage   : 
\& Function: 
\& Returns : true if no SOAP fault
\& Args    :
.Ve
.SS "\fBerrstr()\fP"
.IX Subsection "errstr()"
.Vb 5
\& Title   : errstr
\& Usage   : 
\& Function: 
\& Returns : fault string of SOAP object
\& Args    : none
.Ve
.SS "\fBaccessors()\fP"
.IX Subsection "accessors()"
.Vb 8
\& 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
.Ve
.SS "\fBwebenv()\fP"
.IX Subsection "webenv()"
.Vb 6
\& Title   : webenv
\& Usage   : 
\& Function: contains WebEnv key referencing this
\&           result\*(Aqs session
\& Returns : scalar
\& Args    : none
.Ve
.SS "\fBquery_key()\fP()"
.IX Subsection "query_key()()"
.Vb 6
\& Title   : query_key()
\& Usage   : 
\& Function: contains the web query key assigned
\&           to this result
\& Returns : scalar
\& Args    :
.Ve
.SS "\fBfetch_type()\fP"
.IX Subsection "fetch_type()"
.Vb 5
\& 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
.Ve