Roger Pettett > Bio-Das-ProServer > Bio::Das::ProServer::SourceAdaptor::Transport::martservice

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Module Version: 687   Source  

NAME ^

Bio::Das::ProServer::SourceAdaptor::Transport::martservice - BioMart MartService Transport

VERSION ^

$Revision: 687 $

SYNOPSIS ^

DESCRIPTION ^

This module provides a transport to retrieve data from a BioMart MartService.

SUBROUTINES/METHODS ^

init

Initializes this object using values taken from the configuration.

timeout

Get/set the timeout for requests POSTed via LWP::UserAgent.

martservice

Get/set the MartService URL.

dataset

Get/set the MartService dataset name.

attributes

Get/set the list of attributes to be retrieved from the MartService. This may be specified as an arrayref or a comma-delimited list.

ua

Return a cached LWP::UserAgent object or instantiate a new one.

build_query_xml

Takes a hashref of name/value pairs and returns an XML query string to be POSTed to the MartService.

query

Passed a list of name/value pairs, performs a query against the MartService and returns an arrayref of returned results. Each result is a hashref with keys named after this object's attributes.

DIAGNOSTICS ^

CONFIGURATION AND ENVIRONMENT ^

The following values may be specified in the main configuration file:

martservice

The URL for the BioMart MartService.

dataset

The name of the MartService dataset.

attributes

A comma-separated list of attributes to be retrieved from the BioMart MartService.

timeout

How long (in seconds) to wait for a response from the BioMart MartService.

DEPENDENCIES ^

List::MoreUtils
LWP::UserAgent
XML::Writer

INCOMPATIBILITIES ^

BUGS AND LIMITATIONS ^

AUTHOR ^

Ray Miller <rm7@sanger.ac.uk>

LICENSE AND COPYRIGHT ^

Copyright (c) 2009 Wellcome Trust Sanger Institute

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty.

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