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#
# BioPerl module for Bio::DB::ESoap
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Mark A. Jensen <maj -at- fortinbras -dot- us>
#
# Copyright Mark A. Jensen
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::DB::ESoap - Client for the NCBI Entrez EUtilities SOAP server
=head1 SYNOPSIS
$fac = Bio::DB::ESoap->new( -util => 'esearch' );
$som = $fac->run( -db => 'prot', -term => 'HIV and gp120' );
$fac->set_parameters( -term => 'HIV2 and gp160' );
# accessors corresponding to valid parameters are also created:
$fac->db('nuccore');
$som = $fac->run;
# more later.
=head1 DESCRIPTION
C<ESoap> provides a basic SOAP interface to the NCBI Entrez Utilities
Web Service
(L<http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/DOC/esoap_help.html>).
L<SOAP::Lite> handles the SOAP calls. Higher level access, pipelines,
BioPerl object I/O and such are provided by
L<Bio::DB::SoapEUtilities>.
C<ESoap> complies with L<Bio::ParameterBaseI>. It depends explicitly
on NCBI web service description language files to inform the
C<available_parameters()> method. WSDLs are parsed by a relative
lightweight, Entrez-specific module L<Bio::DB::ESoap::WSDL>.
The C<run()> method returns L<SOAP::SOM> (SOAP Message) objects. No
fault checking or other parsing is performed in this module.
=head1 SEE ALSO
L<Bio::DB::EUtilities>, L<Bio::DB::SoapEUtilities>,
L<Bio::DB::ESoap::WSDL>
=head1 FEEDBACK
=head2 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
=head2 Support
Please direct usage questions or support issues to the mailing list:
L<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.
=head2 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/
=head1 AUTHOR - Mark A. Jensen
Email maj -at- fortinbras -dot- us
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::DB::ESoap;
use strict;
use warnings;
use Bio::Root::Root;
use Bio::DB::ESoap::WSDL;
use SOAP::Lite;
use base qw(Bio::Root::Root Bio::ParameterBaseI);
=head2 new
Title : new
Usage : my $obj = new Bio::DB::ESoap();
Function: Builds a new Bio::DB::ESoap factory
Returns : an instance of Bio::DB::ESoap
Args :
=cut
sub new {
my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($util, $fetch_db, $wsdl) = $self->_rearrange( [qw( UTIL FETCH_DB WSDL_FILE )], @args );
$self->throw("Argument -util must be specified") unless $util;
my @wsdl_pms;
if ($wsdl) {
@wsdl_pms = ( '-wsdl' => $wsdl );
}
else {
$fetch_db ||= 'seq';
my $url = ($util =~ /fetch/ ? 'f_'.$fetch_db : 'eutils');
$url = $NCBI_BASEURL.$WSDL{$url};
@wsdl_pms = ( '-url' => $url );
}
$self->_wsdl(Bio::DB::ESoap::WSDL->new(@wsdl_pms));
$self->_operation($util);
$self->_init_parameters;
$self->_client( SOAP::Lite->new( proxy => $self->_wsdl->service ) );
return $self;
}
=head2 _wsdl()
Title : _wsdl
Usage : $obj->_wsdl($newval)
Function: Bio::DB::ESoap::WSDL object associated with
this factory
Example :
Returns : value of _wsdl (object)
Args : on set, new value (object or undef, optional)
=cut
sub _wsdl {
my $self = shift;
return $self->{'_wsdl'} = shift if @_;
return $self->{'_wsdl'};
}
=head2 _client()
Title : _client
Usage : $obj->_client($newval)
Function: holds a SOAP::Lite object
Example :
Returns : value of _client (a SOAP::Lite object)
Args : on set, new value (a SOAP::Lite object or undef, optional)
=cut
sub _client {
my $self = shift;
return $self->{'_client'} = shift if @_;
return $self->{'_client'};
}
=head2 _operation()
Title : _operation
Alias : util
Usage :
Function: check and convert the requested operation based on the wsdl
Returns :
Args : operation (scalar string)
=cut
sub _operation {
my $self = shift;
my $util = shift;
return $self->{'_operation'} unless $util;
$self->throw("WSDL not yet initialized") unless $self->_wsdl;
my $opn = $self->_wsdl->operations;
if ( grep /^$util$/, keys %$opn ) {
return $self->{'_operation'} = $util;
}
elsif ( grep /^$util$/, values %$opn ) {
my @a = grep { $$opn{$_} eq $util } keys %$opn;
return $self->{'_operation'} = $a[0];
}
else {
$self->throw("Utility '$util' is not recognized");
}
}
sub util { shift->_operation(@_) }
=head2 action()
Title : action
Usage :
Function: return the soapAction associated with the factory's utility
Returns : scalar string
Args : none
=cut
sub action {
my $self = shift;
return $self->{_action} if $self->{_action};
return $self->{_action} = ${$self->_wsdl->operations}{$self->util};
}
=head2 wsdl_file()
Title : wsdl_file
Usage :
Function: get filename of the local WSDL XML copy
Returns : filename (scalar string)
Args : none
=cut
sub wsdl_file {
my $self = shift;
if (ref ($self->_wsdl->wsdl) eq 'File::Temp') {
return $self->_wsdl->wsdl->filename;
}
return $self->_wsdl->wsdl;
}
=head2 run()
Title : _run
Usage : $som = $self->_run(@optional_setting_args)
Function: Call the SOAP service with the factory-associated utility
and parameters
Returns : SOAP::SOM (SOAP Message) object
Args : named parameters appropriate for the utility
Note : no fault checking here
=cut
sub run {
my $self = shift;
my @args = @_;
$self->throw("SOAP::Lite client not initialized") unless
$self->_client;
$self->throw("run requires named args") if @args % 2;
$self->set_parameters(@args) if scalar @args;
my %args = $self->get_parameters;
my @soap_data;
for my $k (keys %args) {
## kludges for NCBI inconsistencies:
my $k_ncbi;
for ($k) {
/QueryKey/ && do {
$k_ncbi = 'query_key';
last;
};
/RetMax/ && do {
$k_ncbi = 'retmax';
last;
};
$k_ncbi = $k;
}
my $data = $args{$k};
next unless defined $data;
for (ref $data) {
/^$/ && do {
push @soap_data, SOAP::Data->name($k_ncbi)->value($data);
last;
};
/ARRAY/ && do {
push @soap_data, SOAP::Data->name($k_ncbi)->value(join(',',@$data));
last;
};
/HASH/ && do {
# for adding multiple data items with the same message
# key (id lists for elink, e.g.)
# see ...::SoapEUtilities, c. line 151
push @soap_data, map {
SOAP::Data->name($k_ncbi)->value($_)
} keys %$data;
};
}
}
$self->_client->on_action( sub { $self->action } );
my $som = $self->_client->call( $self->util,
@soap_data );
return $som;
}
sub _result_elt_name { my $s=shift; (keys %{$s->_wsdl->response_parameters($s->util)})[0] };
sub _response_elt_name { shift->_result_elt_name }
sub _request_elt_name { my $s=shift; (keys %{$s->_wsdl->request_parameters($s->util)})[0] };
=head2 Bio::ParameterBaseI compliance
=cut
sub available_parameters {
my $self = shift;
my @args = @_;
return @{$self->_init_parameters};
}
sub set_parameters {
my $self = shift;
my @args = @_;
$self->throw("set_parameters requires named args") if @args % 2;
($_%2 ? 1 : $args[$_] =~ s/^-//) for (0..$#args);
my %args = @args;
# special translations :
if ( defined $args{'usehistory'} ) {
$args{'usehistory'} = ($args{'usehistory'} ? 'y' : undef);
}
$self->_set_from_args(\%args, -methods=>$self->_init_parameters);
return $self->parameters_changed(1);
}
sub get_parameters {
my $self = shift;
my @ret;
foreach (@{$self->_init_parameters}) {
next unless defined $self->$_();
push @ret, ($_, $self->$_());
}
return @ret;
}
sub reset_parameters {
my $self = shift;
my @args = @_;
$self->throw("reset_parameters requires named args") if @args % 2;
($_%2 ? 1 : $args[$_] =~ s/^-//) for (0..$#args);
my %args = @args;
my %reset;
@reset{@{$self->_init_parameters}} = (undef) x @{$self->_init_parameters};
$reset{$_} = $args{$_} for keys %args;
$self->_set_from_args( \%reset, -methods => $self->_init_parameters );
$self->parameters_changed(1);
return 1;
}
=head2 parameters_changed()
Title : parameters_changed
Usage : $obj->parameters_changed($newval)
Function: flag to indicate, well, you know
Example :
Returns : value of parameters_changed (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub parameters_changed {
my $self = shift;
return $self->{'parameters_changed'} = shift if @_;
return $self->{'parameters_changed'};
}
=head2 _init_parameters()
Title : _init_parameters
Usage : $fac->_init_parameters
Function: identify the available input parameters
using the wsdl object
Returns : arrayref of parameter names (scalar strings)
Args : none
=cut
sub _init_parameters {
my $self = shift;
return $self->{_params} if $self->{_params};
$self->throw("WSDL not yet initialized") unless $self->_wsdl;
my $phash = {};
my $val = (values %{$self->_wsdl->request_parameters($self->util)})[0];
$$phash{$_} = undef for map { keys %$_ } @{$val};
my $params =$self->{_params} = [sort keys %$phash];
# create parm accessors
$self->_set_from_args( $phash,
-methods => $params,
-create => 1,
-code =>
'my $self = shift;
if (@_) {
$self->parameters_changed(1);
return $self->{\'_\'.$method} = shift;
}
$self->parameters_changed(0);
return $self->{\'_\'.$method};' );
$self->parameters_changed(1);
return $self->{_params};
}
1;
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