#$Id: Central.pm,v 1.8 2009/03/31 21:19:36 kawas Exp $
package MOBY::Client::Central;
use SOAP::Lite;
#use SOAP::Lite + trace; # for debugging
use strict;
use Carp;
use XML::LibXML;
use MOBY::MobyXMLConstants;
use MOBY::Client::ServiceInstance;
use MOBY::Client::Registration;
use MOBY::Client::SimpleArticle;
use MOBY::Client::CollectionArticle;
use MOBY::Client::SecondaryArticle;
use MOBY::Client::OntologyServer;
use vars qw($AUTOLOAD @ISA $MOBY_server $MOBY_uri);
use vars qw /$VERSION/;
$VERSION = sprintf "%d.%02d", q$Revision: 1.8 $ =~ /: (\d+)\.(\d+)/;
=head1 NAME
MOBY::Client::Central - a client side wrapper for MOBY Central
=cut
=head1 SYNOPSIS
use MOBY::Client::Central;
my $Central = MOBY::Client::Central->new();
my ($Services, $REG) = $Central->findService(
input =>[
[DNASequence => ['NCBI_gi', 'NCBI_Acc']],
],
expandObjects => 1
);
unless ($Services){
print "Service discovery failed with the following errror: ";
print $REG->message;
end
}
foreach my $SERVICE(@{$Services}){
print "Service Name: ", $SERVICE->name, "\n";
print "Service Provider: ", $SERVICE->authority,"\n";
}
=cut
=head1 DESCRIPTION
Client side "wrapper" for communicating with
the MOBY::Central registry.
Used to do various read-only transactions with MOBY-Central. Parses
MOBY::Central XML output into Perlish lists, hashes, and objects. This should
be sufficient for most or all MOBY Client activities written in Perl.
=cut
=head1 AUTHORS
Mark Wilkinson (markw@illuminae.com)
BioMOBY Project: http://www.biomoby.org
=cut
=head1 METHODS
=head2 new
Usage : my $MOBY = MOBY::Client::Central->new(Registries => \%regrefs)
Function : connect to one or more MOBY-Central
registries for searching
Returns : MOBY::Client::Central object
ENV & PROXY : you can set environment variables to change the defaults.
By default, a call to 'new' will initialize MOBY::Client::Central
to connect to the default MOBY Central registry. The location of
this registry can be determined by examining the redirect from:
http://biomoby.org/mobycentral
If you wish to chose another registry by default, or if you need
to set up additional connection details (e.g. PROXY) then you may
set the following environment variables to whatever you
require:
MOBY_SERVER (default http://moby.ucalgary.ca/moby/MOBY-Central.pl)
MOBY_URI (default http://moby.ucalgary.ca/MOBY/Central)
MOBY_PROXY (no default)
Args : user_agent - optional. The name of your software application
Registries - optional.
- takes the form
{$NAME1 => {
URL => $URL,
URI => $URI,
PROXY => $proxy_server},
$NAME2 => {
URL => $URL,
URI => $URI,
PROXY => $proxy_server},
}
- by default this becomes
{mobycentral => {
URL => 'http://moby.ucalgary.ca/moby/MOBY-Central.pl',
URI => 'http://moby.ucalgary.ca/MOBY/Central'}
}
Discussion: Each registry must have a different
NAME. If you have more than one
registry with the same NAME, only
one will be used. You can NAME them
however you please - this is for
internal reference only. You will
make subsequent calls on one or more
of these registries by NAME, or by
default on all registries.
Notes : BE CAREFUL WITH OBJECT/SERVICE
REGISTRATION!! YOU WILL REGISTER
IN EVERY MOBY-CENTRAL YOU HAVE
NAMED! If you do not host a MOBY::Central
database locally, or don't know
better,then don't use any arguments
at all, and everything should work
=cut
my $debug = 0;
if ($debug) {
open( OUT, ">/tmp/CentralLogOut.txt" )
|| die "cant open logfile CentralLogOut.txt $!\n";
close OUT;
}
{
# Encapsulated:
# DATA
#___________________________________________________________
#ATTRIBUTES
my %_attr_data = # DEFAULT ACCESSIBILITY
(
Connections => [ undef, 'read/write' ],
default_MOBY_servername => [ 'mobycentral', 'read/write' ],
default_MOBY_server => [ '', 'read/write'],
default_MOBY_uri => [ 'http://biomoby.org/MOBY/Central', 'read/write' ],
default_MOBY_proxy => [ undef, 'read/write' ],
default_MOBY_type => [ 'soap', 'read/write' ],
Registries => [ undef, 'read/write' ],
multiple_registries => [ undef, 'read/write' ],
user_agent => [ "MOBY-Client-Central", 'read/write'],
# SWITCH TO THESE FOR A LOCAL MOBY CENTRAL REGISTRY
#default_MOBY_server => ['http://localhost/cgi-bin/MOBY-Central.pl', 'read/write'],
#default_MOBY_uri => ['http://localhost/MOBY/Central', 'read/write'],
);
#_____________________________________________________________
# METHODS, to operate on encapsulated class data
# Is a specified object attribute accessible in a given mode
sub _accessible {
my ( $self, $attr, $mode ) = @_;
return 0 unless ( $mode && $_attr_data{$attr} );
$_attr_data{$attr}[1] =~ /$mode/;
}
# Classwide default value for a specified object attribute
sub _default_for {
my ( $self, $attr ) = @_;
$_attr_data{$attr}[0];
}
# List of names of all specified object attributes
sub _standard_keys {
keys %_attr_data;
}
sub Connection {
my ( $self, $desired ) = @_;
if ($desired) {
my @registries = @{$self->Connections};
foreach (@registries){
my ( $name, $type, $connect ) = @{$_};
return ( $type, $connect ) if $name eq $desired;
}
}
else {
my ( $name, $type, $connect ) = @{ $self->Connections->[0] };
return ( $type, $connect );
}
return ( undef, undef );
}
}
sub _call {
# this method replaces the former calls directly
# to teh SOAP_Connection, to give more flexibility
# in how that call is made
# most subroutines in here do the following:
# $return = $self->SOAP_connection->call(registerObjectClass => ($message))->paramsall;
# or $payload = $self->SOAP_connection($reg)->call('Relationships' => ($m))->paramsall;
# so intercept that and figure out if we are actually making a SOAP call or not
# and determine which registry it is
my ( $self, $reg, $method, @params ) = @_;
$reg = $self->default_MOBY_servername if $reg eq "default";
$reg = $self->default_MOBY_servername if !$reg;
my ( $type, $connect ) = $self->Connection($reg);
return "<result>EXECUTION ERROR - registry $reg not found</result>"
unless ( $type && $connect );
my $param = join "", @params; # must be a single message!
if ( lc($type) eq "get" ) {
#print STDERR "executing CGI call\n";
use LWP::UserAgent;
my $ua = LWP::UserAgent->new;
$ua->agent($self->user_agent);
use CGI;
$param =~ s/([^a-zA-Z0-9_\-.])/uc sprintf("%%%02x",ord($1))/eg;
my $paramstring = "?action=$method";
$paramstring .= ";payload=$param" if $param;
my $req = HTTP::Request->new( GET => $connect . $paramstring );
my $res = $ua->request($req);
if ( $res->is_success ) {
return $res->content;
}
else {
return
"<result>EXECUTION ERROR - unsuccessful call to MOBY Central registry named '$reg'</result>";
}
}
else {
#print STDERR "executing SOAP call\n";
my @payload = $connect->call( $method => SOAP::Data->type('string' => $param ) )->paramsall;
return @payload;
}
}
sub new {
my ( $caller, %args ) = @_;
my $caller_is_obj = ref($caller);
return $caller if $caller_is_obj;
my $class = $caller_is_obj || $caller;
my $proxy;
my $self = bless {}, $class;
foreach my $attrname ( $self->_standard_keys ) {
if ( exists $args{$attrname} ) {
$self->{$attrname} = $args{$attrname};
}
elsif ($caller_is_obj) {
$self->{$attrname} = $caller->{$attrname};
}
else {
$self->{$attrname} = $self->_default_for($attrname);
}
}
$self->Connections( [] ); # initialize;
do {
my ($central, $ontologyserver) = _getDefaultCentral();
$self->default_MOBY_server($central) if $central;
} unless $ENV{MOBY_SERVER};
# if user has set up preferred servers, then use those by default
$self->default_MOBY_server( $ENV{MOBY_SERVER} ) if $ENV{MOBY_SERVER};
$self->default_MOBY_uri( $ENV{MOBY_URI} ) if $ENV{MOBY_URI};
$self->default_MOBY_type( $ENV{MOBY_TYPE} ) if $ENV{MOBY_TYPE};
$self->default_MOBY_proxy( $ENV{MOBY_PROXY} ) if $ENV{MOBY_PROXY};
if ( $self->Registries ) {
my $regno = 0;
my %reg = %{ $self->Registries };
while ( my ( $name, $acc ) = each %reg ) {
$self->default_MOBY_servername($name); # set the current as the default... if there is only one, then it becomes default, which is nice! If ther eis more than one, then the person shold be explicitly calling one or the other anyway
$regno++; # count how many registries we have in total
my $url = $acc->{URL} ? $acc->{URL} : $self->default_MOBY_server;
my $uri = $acc->{URI} ? $acc->{URI} : $self->default_MOBY_uri;
my $type = $acc->{TYPE} ? $acc->{TYPE} : $self->default_MOBY_type;
my $proxy = $acc->{PROXY} ? $acc->{PROXY} : $self->default_MOBY_proxy;
$type ||= 'soap';
if ( lc($type) eq "get" ) {
push @{ $self->Connections }, [ $name, $type, $url ];
}
else {
my @soapargs;
if ($proxy) {
@soapargs = ( $url, proxy => [ 'http' => $proxy ], user_agent => $self->user_agent, );
}
else {
@soapargs = ($url);
}
push @{ $self->Connections },
[
$name, $type,
SOAP::Lite->proxy(@soapargs, agent=>$self->user_agent )->uri($uri)->on_fault(
sub {
my ( $soap, $res ) = @_;
die ref $res
? ("\nConnection to MOBY Central at '$uri' died because:\n\t" . $res->faultstring)
: ("Failed with status:" . $soap->transport->status),
"\n ERROR ERROR ERROR\n";
}
)
];
}
} # Done iterating over multiple registries
$self->multiple_registries( $regno - 1 )
; # one is not "multiple", it is just a change in default -> set to "false" if only one
}
else { # no registries specified
$self->multiple_registries(0);
if ( lc( $self->default_MOBY_type ) eq "get" ) {
push @{ $self->Connections },
[
$self->default_MOBY_servername, $self->default_MOBY_type,
$self->default_MOBY_server
];
}
else {
$self->Registries(
{
$self->default_MOBY_servername => {
URL => $self->default_MOBY_server,
URI => $self->default_MOBY_uri
}
}
);
my @soapargs;
if ( $self->default_MOBY_proxy ) {
@soapargs = (
$self->default_MOBY_server,
proxy => [ 'http' => $self->default_MOBY_proxy ]
);
}
else {
@soapargs = ( $self->default_MOBY_server );
}
push @{ $self->Connections },
[
$self->default_MOBY_servername,
$self->default_MOBY_type,
SOAP::Lite->proxy(@soapargs, agent=>$self->user_agent )->uri( $self->default_MOBY_uri )
->on_fault(
sub {
my ( $soap, $res ) = @_;
die ref $res
? ("\nConnection to default MOBY Central died because:\n\t" . $res->faultstring)
: ("Failed with status:" . $soap->transport->status),
"\n ERROR ERROR ERROR\n";
}
)
];
}
}
return undef unless $self->Connection(); # gotta have at least one...
return $self;
}
sub _getDefaultCentral {
use LWP::UserAgent;
use HTTP::Request::Common qw(HEAD);
my $ua = LWP::UserAgent->new;
my $req = HEAD 'http://biomoby.org/mobycentral';
my $res = $ua->simple_request($req);
my $mobycentral = $res->header('location');
$req = HEAD 'http://biomoby.org/ontologyserver';
$res = $ua->simple_request($req);
my $ontologyserver = $res->header('location');
return ($mobycentral, $ontologyserver);
}
=head2 registerObject a.k.a registerObjectClass
Usage : $REG = $MOBY->registerObject(%args)
Usage : $REG = $MOBY->registerObjectClass(%args)
Function : register a new type of MOBY Object
Returns : MOBY::Registration object
Args : objectType => "the name of the Object"
description => "a human-readable description of the object"
contactEmail => "your@email.address"
authURI => "URI of the registrar of this object"
Relationships => {
relationshipType1 => [
{object => Object1,
articleName => ArticleName1},
{object => Object2,
articleName => ArticleName2}
],
relationshipType2 => [
{object => Object3,
articleName => ArticleName3}
]
}
=cut
sub registerObjectClass {
my ( $self, %a ) = @_;
return $self->registerObject(%a);
}
sub registerObject {
my ( $self, %a ) = @_;
return $self->errorRegXML(
"Function not allowed when querying multiple registries")
if $self->multiple_registries;
return $self->errorRegXML(
"Contact email address (contactEmail parameter) is required for object registration"
)
if ( !$a{contactEmail} );
my $term = $a{'objectType'} || "";
my $desc = $a{'description'} || "";
if ( $desc =~ /<!\[CDATA\[((?>[^\]]+))\]\]>/ ) {
$desc = $1;
}
my $contactEmail = $a{'contactEmail'} || "";
my $authURI = $a{'authURI'} || "";
my %Relationships = %{ $a{'Relationships'} };
my $clobber = $a{'Clobber'} ? $a{'Clobber'} : 0;
my $message = "<registerObjectClass>
<objectType>$term</objectType>
<Description><![CDATA[$desc]]></Description>
<authURI>$authURI</authURI>
<contactEmail>$contactEmail</contactEmail>
<Clobber>$clobber</Clobber>\n";
while ( my ( $type, $objlistref ) = each %Relationships ) {
$message .= "<Relationship relationshipType='$type'>\n";
foreach my $objnamepair ( @{$objlistref} ) {
my $object = $objnamepair->{object};
my $article = $objnamepair->{articleName};
return $self->errorRegXML(
"Object name missing from one of your $type relationships")
unless ($object);
$article ||= "";
$message .=
"<objectType articleName='$article'>$object</objectType>\n";
}
$message .= "</Relationship>\n";
}
$message .= "</registerObjectClass>";
# my $return = $self->SOAP_connection->call(registerObjectClass => ($message))->paramsall;
my ($return) = $self->_call( 'default', 'registerObjectClass', $message );
return ( $self->parseRegXML($return) );
}
=head2 deregisterObject a.k.a. deregisterObjectClass
Usage : $REG = $MOBY->deregisterObject(%args)
Usage : $REG = $MOBY->deregisterObjectClass(%args)
Function : deregister a MOBY Object
Returns : MOBY::Registration object
Args : objectType => $objectName (from Object ontology)
=cut
sub deregisterObjectClass {
my ( $self, %a ) = @_;
return $self->deregisterObject(%a);
}
sub deregisterObject {
my ( $self, %a ) = @_;
return $self->errorRegXML(
"Function not allowed when querying multiple registries")
if $self->multiple_registries;
my $id = $a{'objectType'} || "";
my $message = "
<deregisterObjectClass>
<objectType>$id</objectType>
</deregisterObjectClass>";
# my $return = $self->SOAP_connection->call(deregisterObjectClass => ($message))->paramsall;
my ($return) = $self->_call( 'default', 'deregisterObjectClass', $message );
return ( $self->parseRegXML($return) );
}
=head2 registerServiceType
Usage : $REG = $MOBY->registerServiceType(%args)
Function : register a new MOBY Service type
Returns : MOBY::Registration object
Args : serviceType => $serviceType
description => "human readable description"
Relationships => {$relationshipType1 => \@services,
$relationshipType2 => \@services}
contactEmail => "your@email.address.here"
authURI => "your.authority.info"
=cut
sub registerServiceType {
my ( $self, %a ) = @_;
return $self->errorRegXML(
"Function not allowed when querying multiple registries")
if $self->multiple_registries;
my $type = $a{'serviceType'} || "";
my $desc = $a{'description'};
if ( $desc =~ /<!\[CDATA\[((?>[^\]]+))\]\]>/ ) {
$desc = $1;
}
$desc ||= "";
my $email = $a{'contactEmail'} || "";
my $auth = $a{'authURI'} || "";
my %Relationships = %{ $a{'Relationships'} };
my $message = "
<registerServiceType>
<serviceType>$type</serviceType>
<Description><![CDATA[$desc]]></Description>
<contactEmail>$email</contactEmail>
<authURI>$auth</authURI>\n";
while ( my ( $type, $servlistref ) = each %Relationships ) {
$message .= "<Relationship relationshipType='$type'>\n";
foreach my $servicetype ( @{$servlistref} ) {
$message .= "<serviceType>$servicetype</serviceType>\n";
}
$message .= "</Relationship>\n";
}
$message .= "</registerServiceType>";
# my $return = $self->SOAP_connection->call(registerServiceType => ($message))->paramsall;
my ($return) = $self->_call( 'default', 'registerServiceType', $message );
return ( $self->parseRegXML($return) );
}
=head2 deregisterServiceType
Usage : $REG = $MOBY->deregisterServiceType(%args)
Function : deregister a deprecated MOBY Service Type
Returns : MOBY::Registration object
Args : serviceType => $serviceType (from ontology)
=cut
sub deregisterServiceType {
my ( $self, %a ) = @_;
return $self->errorRegXML(
"Function not allowed when querying multiple registries")
if $self->multiple_registries;
my $id = $a{'serviceType'} || "";
my $message = "
<deregisterServiceType>
<serviceType>$id</serviceType>
</deregisterServiceType>";
# my $return = $self->SOAP_connection->call(deregisterServiceType => ($message))->paramsall;
my ($return) = $self->_call( 'default', 'deregisterServiceType', $message );
return ( $self->parseRegXML($return) );
}
=head2 registerNamespace
Usage : $REG = $MOBY->registerNamespace(%args)
Function : register a new Namespace
Returns : MOBY::Registration object
Args : namespaceType => $namespaceType (required)
authURI => your.authority.URI (required)
description => "human readable description of namespace" (required)
contactEmail => "your@address.here" (required)
=cut
sub registerNamespace {
my ( $self, %a ) = @_;
return $self->errorRegXML(
"Function not allowed when querying multiple registries")
if $self->multiple_registries;
my $type = $a{'namespaceType'} || "";
my $authURI = $a{'authURI'} || "";
my $desc = $a{'description'};
if ( $desc =~ /<!\[CDATA\[((?>[^\]]+))\]\]>/ ) {
$desc = $1;
}
$desc ||= "";
my $contact = $a{'contactEmail'} || "";
my $message = "
<registerNamespace>
<namespaceType>$type</namespaceType>
<Description><![CDATA[$desc]]></Description>
<authURI>$authURI</authURI>
<contactEmail>$contact</contactEmail>
</registerNamespace>";
# my $return = $self->SOAP_connection->call(registerNamespace => ($message))->paramsall;
my ($return) = $self->_call( 'default', 'registerNamespace', $message );
return ( $self->parseRegXML($return) );
}
=head2 deregisterNamespace
Usage : $REG = $MOBY->deregisterNamespace(%args)
Function : deregister a deprecated MOBY Namespace
Returns : MOBY::Registration object
Args : namespaceType => $mynamespaceType (from ontology)
=cut
sub deregisterNamespace {
my ( $self, %a ) = @_;
return $self->errorRegXML(
"Function not allowed when querying multiple registries")
if $self->multiple_registries;
my $id = $a{'namespaceType'} || "";
my $message = "
<deregisterNamespace>
<namespaceType>$id</namespaceType>
</deregisterNamespace>";
# my $return = $self->SOAP_connection->call(deregisterNamespace => ($message))->paramsall;
my ($return) = $self->_call( 'default', 'deregisterNamespace', $message );
return ( $self->parseRegXML($return) );
}
=head2 registerService
Usage : $REG = $MOBY->registerService(%args)
Function : register a new MOBY Service instance
Returns : MOBY::Registration object
Common Required Args :
serviceName => $serviceName,
serviceType => $serviceType,
authURI => $authURI,
contactEmail => "your@mail.address",
description => $human_readable_description,
category => "moby" | "cgi-async" | "cgi" | "moby-async" | "doc-literal" | "doc-literal-async"
URL => $URL_TO_SERVICE (or URL to WSDL document for wsdl-type services)
input: listref; (articleName may be undef)
input =>[
[articleName1,[objType1 => \@namespaces]], # Simple
[articleName2, [[objType2 => \@namespaces]]], # collection of one object type
[articleName3,[[objType3 => \@namespaces],
[objType4 => \@namespaces]]] # collection of multiple object types
]
output: listref; (articleName may be undef)
output =>[
[articleName1,[objType1 => \@namespaces]], # Simple
[articleName2,[[objType2 => \@namespaces]]], # collection of one object type
[articleName3,[[objType3 => \@namespaces],
[objType4 => \@namespaces]]] # collection of multiple object types
]
secondary: hashref
secondary => {parametername1 => {
datatype => TYPE,
description => "cutoff value",
default => DEFAULT,
max => MAX,
min => MIN,
enum => [one, two]},
parametername2 => {
datatype => TYPE,
description => "e-value",
default => DEFAULT,
max => MAX,
min => MIN,
enum => [one, two]}
}
=cut
sub registerService {
my ( $self, %a ) = @_;
return $self->errorRegXML(
"Function not allowed when querying multiple registries")
if $self->multiple_registries;
my $name = $a{serviceName} || "";
my $type = $a{serviceType} || "";
my $authURI = $a{authURI} || "";
my $email = $a{contactEmail} || "";
my $URL = $a{URL} || "";
my $desc = $a{description} || "";
if ( $desc =~ /<!\[CDATA\[((?>[^\]]+))\]\]>/ ) {
$desc = $1;
}
#TODO ensure that sigURL and URL are valid urls
# ^(([^:/?#]+):)?(//([^/?#]*))?([^?#]*)(\?([^#]*))? <- matches any uri
# ^((([^:/?#]+):)?(//)?[\w]+\.[\w](\.[w])*((\/|\.)?[\w]+)*)$ <- my version
my $signatureURL = $a{signatureURL} || "";
my $Category = lc( $a{category} );
chomp $Category;
$Category ||= "";
#____________call RDFagent__________________________________________________
if ( $signatureURL ne "" ) {
my $ch = 0;
my $sign_req;
foreach $sign_req ( $name, $type, $authURI, $email, $URL, $desc,
$Category )
{
if ( $sign_req ne "" ) {
$ch = 1;
}
}
if ( $ch == 0 ) {
# print "call Agent\n";
my $message = "
<registerService>
<Category></Category>
<serviceName></serviceName>
<serviceType></serviceType>
<Description></Description>
<signatureURL>$signatureURL</signatureURL>
<URL></URL>
<authURI></authURI>
<contactEmail></contactEmail>
</registerService>";
my ($return) =
$self->_call( 'default', 'registerService', $message );
return ( $self->parseRegXML($return) );
}
}
#____________________________________________________________________________________________
return $self->errorRegXML(
"Only 'moby', 'cgi', 'cgi-async', 'moby-async', 'doc-literal', 'doc-literal-async' Service Categories are currently allowed - you gave me $Category"
)
unless ( ( $Category eq 'moby' )
|| ( $Category eq 'moby-async' )
|| ( $Category eq 'cgi-async' )
|| ( $Category eq 'doc-literal' )
|| ( $Category eq 'doc-literal-async' )
|| ( $Category eq 'cgi' ));
return $self->errorRegXML(
"All Fields Required: serviceName, serviceType, authURI, contactEmail, URL, description, Category, input, output, secondary"
)
unless ( $name
&& $type
&& $authURI
&& $email
&& $URL
&& $desc
&& $Category );
my $message = "
<registerService>
<Category>$Category</Category>
<serviceName>$name</serviceName>
<serviceType>$type</serviceType>
<Description><![CDATA[$desc]]></Description>
<signatureURL>$signatureURL</signatureURL>
<URL>$URL</URL>
<authURI>$authURI</authURI>
<contactEmail>$email</contactEmail>";
my %SEC;
if ( $a{'secondary'} && ( ref( $a{'secondary'} ) eq 'HASH' ) ) {
%SEC = %{ $a{secondary} };
}
elsif ( $a{'secondary'} && ( ref( $a{'secondary'} ) ne 'HASH' ) ) {
return $self->errorRegXML(
"invalid structure of secondary parameters. Expected hashref."
);
}
my %funkyhash = ( Input => $a{input}, Output => $a{output} );
while ( my ( $inout, $param ) = each %funkyhash ) {
my $inout_lc = lc($inout);
my @ALLARTICLES = @{$param};
$message .= "<${inout_lc}Objects><${inout}>\n";
# input =>[
# [articleName1,[objType1 => \@namespaces]], # Simple
# [articleName2, [[objType2 => \@namespaces]]], # collection of one object type
# [articleName3,[[objType3 => \@namespaces],
# [objType4 => \@namespaces]]] # collection of multiple object types (THIS IS NOW ILLEGAL!)
# ]
foreach my $article (@ALLARTICLES) {
my ( $articleName, $def ) = @{$article};
$articleName ||= "";
my @Objects; #
unless ( ref($def) eq 'ARRAY') { # $def = [objType => \@ns] or $def=[[objType => \@ns]]
return $self->errorRegXML("invalid structure of $inout objects, expected SINGLE arrayref for article $articleName as required by the 0.86 API");
}
my @objectdefs;
if ( ( ref $def->[0] ) eq 'ARRAY' ) { # collection $def->[0] = [objType => \@ns]
# def= [[objType2 => [ns3, ns4...]], ...]
$message .= "<Collection articleName='$articleName'>\n";
if (scalar(@{$def->[0]} > 2)){
return $self->errorRegXML("invalid structure of $inout objects. Collections may not have more than one Simple content type as per API version 0.86");
}
@objectdefs = @{$def};
if (scalar(@objectdefs) > 1){
return $self->errorRegXML("invalid structure of $inout objects. Collections may not have more than one Simple content type as per API version 0.86");
}
} else { # Simple $def->[0] = objType
# def = [objType1 => [ns1, ns2...]],
@objectdefs = ($def);
}
foreach my $objectdef (@objectdefs) {
if ( ref( $def->[0] ) eq 'ARRAY' ) {
$message .= "<Simple>\n";
}
else {
$message .= "<Simple articleName='$articleName'>\n";
}
my ( $type, $Namespaces ) = @{$objectdef};
$type ||= "";
$message .= "<objectType>$type</objectType>\n";
unless ( ref($Namespaces) eq 'ARRAY' ) {
return $self->errorRegXML(
"invalid structure of $inout namespaces for object $type in article $articleName; expected arrayref"
);
}
foreach my $ns ( @{$Namespaces} ) {
$message .= "<Namespace>$ns</Namespace>\n";
}
$message .= "</Simple>\n";
}
if ( ref( $def->[0] ) eq 'ARRAY' ) {
$message .= "</Collection>\n";
}
}
$message .= "</${inout}></${inout_lc}Objects>\n";
}
# secondary => {parametername1 => {datatype => TYPE,
# default => DEFAULT,
# max => MAX,
# min => MIN,
# enum => [one, two]},
# parametername2 => {datatype => TYPE,
# default => DEFAULT,
# max => MAX,
# min => MIN,
# enum => [one, two]}
# }
#
$message .= "<secondaryArticles>\n";
while ( my ( $param, $desc ) = each %SEC ) {
unless ( ref($desc) eq 'HASH' ) {
return $self->errorRegXML( "invalid structure of secondary article $param; expected hashref of limitations"
);
}
my %data = %{$desc};
my $default = defined($data{default})?$data{default}:"";
my $max = defined($data{max})?$data{max}:"";
my $min = defined($data{min})?$data{min}:"";
my $descr = defined($data{description})?$data{description}:"";
my $datatype = $data{datatype} || "";
my $enums = $data{enum} || [];
unless ($datatype) {
return $self->errorRegXML("a secondaryArticle must contain at least a datatype value in secondary article $param"
);
}
unless ( $datatype =~ /Integer|Float|String|DateTime|Boolean/ )
{
return $self->errorRegXML("a secondaryArticle must have a datatype of Integer, Float, String, Boolean or DateTime"
);
}
unless ( ref($enums) eq 'ARRAY' ) {
return $self->errorRegXML("invalid structure of enum limits in secondary article $param; expected arrayref"
);
}
my @enums = @{$enums};
$message .= "<Parameter articleName='$param'>\n";
$message .= "<default>$default</default>\n";
$message .= "<description>$descr</description>\n";
$message .= "<datatype>$datatype</datatype>\n";
$message .= "<max>$max</max>\n";
$message .= "<min>$min</min>\n";
foreach (@enums) {
$message .= "<enum>$_</enum>\n";
}
$message .= "</Parameter>\n";
}
$message .= "</secondaryArticles>\n";
$message .= "</registerService>";
$debug && &_LOG(" message\n\n$message\n\n");
my ($return) = $self->_call( 'default', 'registerService', $message );
#_______call a new version RDFbuilder (by Eddie Kawas) _________________________________________
my $reg = $self->parseRegXML($return);
return $reg;
#_______________________________________________________________________________________________
}
=head2 registerServiceWSDL
Usage : Needs documentation
=cut
sub registerServiceWSDL {
my ( $self, %a ) = @_;
return $self->errorRegXML(
"Function not allowed when querying multiple registries")
if $self->multiple_registries;
my $message = "";
# my $return = $self->SOAP_connection->call(registerServiceWSDL => ($message))->paramsall;
my ($return) = $self->_call( 'default', 'registerServiceWSDL', $message );
return ( $self->parseRegXML($return) );
}
=head2 deregisterService
Usage : $REG = $MOBY->deregisterService(%args)
Function : deregister a registered MOBY Service
Returns : MOBY::Registration object
Args : serviceName => $serviceID, authURI => $authority
=cut
sub deregisterService {
my ( $self, %a ) = @_;
return $self->errorRegXML(
"Function not allowed when querying multiple registries")
if $self->multiple_registries;
my $name = $a{'serviceName'};
my $auth = $a{'authURI'};
( defined($name) && defined($auth) ) || return (
&parseRegXML( "
<MOBYRegistration>
<id></id>
<success>0</success>
<message><![CDATA[you did not pass a valid service Identifier]]></message>
</MOBYRegistration>" )
);
my $message = "
<deregisterService>
<serviceName>$name</serviceName>
<authURI>$auth</authURI>
</deregisterService>";
# my $return = $self->SOAP_connection->call(deregisterService => ($message))->paramsall;
my ($return) = $self->_call( 'default', 'deregisterService', $message );
return ( $self->parseRegXML($return) );
}
=head2 findService
Usage : ($ServiceInstances, $RegObject) = $MOBY->findService(%args)
Function : Find services that match certain search criterion
Returns : ON SUCCESS: arrayref of MOBY::Client::ServiceInstance objects, and undef
ON FAILURE: undef, and a MOBY::Registration object indicating the reason for failure
Args :
Registry => which registry do you want to search (optional)
serviceName => $serviceName, (optional)
serviceType => $serviceType, (optional)
authURI => $authURI, (optional)
authoritative => 1, (optional)
category => "moby" | "cgi" | "moby-async" (optional)
expandObjects => 1, (optional)
expandServices => 1, (optional)
URL => $URL_TO_SERVICE (optional)
keywords => [kw1, kw2, kw3] (optional)
input =>[ (optional)
[objType1 => [ns1, ns2...]], # Simple
[[objType2 => [ns3, ns4...]]], # collection of one object type
[[objType3 => [ns3, ns4...]],
[objType4 => [ns5, ns6...]]], # collection of multiple object types
]
output =>[ (optional)
[objType1 => [ns1, ns2...]], # Simple
[[objType2 => [ns3, ns4...]]], # collection of one object type
[[objType3 => [ns3, ns4...]],
[objType4 => [ns5, ns6...]]], # collection of multiple object types
]
=cut
sub findService {
my ( $self, %a ) = @_;
my $reg = ( $a{Registry} ) ? $a{Registry} : $self->default_MOBY_servername;
my $id = $a{'serviceID'};
my $servicename = $a{'serviceName'} || "";
my $authoritative = $a{'authoritative'} || "";
my $serviceType = $a{'serviceType'} || "";
my $authURI = $a{'authURI'} || "";
my $category = $a{'category'} || "";
my $exObj = $a{'expandObjects'} || 0;
my $exServ = $a{'expandServices'} || 0;
my $kw = $a{'keywords'} || [];
ref($kw) eq 'ARRAY' || return (
undef,
$self->errorRegXML(
"invalid structure of keywords. Expected arrayref"
)
);
my @kw = @{$kw};
my $message = "<findService>\n";
defined($authoritative)
&& ( $message .= "<authoritative>$authoritative</authoritative>\n" );
$category && ( $message .= "<Category>$category</Category>\n" );
$serviceType && ( $message .= "<serviceType>$serviceType</serviceType>\n" );
$servicename && ( $message .= "<serviceName>$servicename</serviceName>\n" );
$authURI && ( $message .= "<authURI>$authURI</authURI>\n" );
defined($exObj)
&& ( $message .= "<expandObjects>$exObj</expandObjects> \n" );
defined($exServ)
&& ( $message .= "<expandServices>$exServ</expandServices>\n" );
if ( scalar(@kw) ) {
$message .= " <keywords>\n";
foreach my $kwd (@kw) {
$message .= "<keyword>$kwd</keyword>\n";
}
$message .= "</keywords>\n";
}
#$a{input} = [[]] unless (defined $a{input});
#$a{output} = [[]] unless (defined $a{output});
if ( defined $a{input} && ( ref( $a{input} ) ne 'ARRAY' ) ) {
return (
undef,
$self->errorRegXML(
"invalid structure of input objects, expected arrayref for input"
)
);
}
if ( defined $a{output} && ( ref( $a{output} ) ne 'ARRAY' ) ) {
return (
undef,
$self->errorRegXML(
"invalid structure of output objects, expected arrayref for output"
)
);
}
my %funkyhash;
$funkyhash{Input} = $a{input} if ( defined $a{input} );
$funkyhash{Output} = $a{output} if ( defined $a{output} );
#input =>[
# [objType1 => [ns1, ns2...]], # Simple
# [[objType2 => [ns3, ns4...]]], # collection of one object type
# [[objType3 => [ns3, ns4...]],
# [objType4 => [ns5, ns6...]]], # collection of multiple object types
# ]
while ( my ( $inout, $param ) = each %funkyhash ) {
die "no inout parameter from teh funkyhash" unless defined $inout;
die "no param parameter from teh funkyhash" unless defined $param;
die "param parameter should be a listref"
unless ( ref($param) eq 'ARRAY' );
my $inout_lc = lc($inout);
my @PARAM = @{$param};
$message .= "<${inout_lc}Objects><${inout}>\n";
foreach my $param (@PARAM) {
unless ( ref($param) eq 'ARRAY' ) {
return (
undef,
$self->errorRegXML(
"invalid structure of $inout objects, expected arrayref of class and \@namespaces"
)
);
}
my ( $class, $namespaces ) = @{$param};
die "no class part of param " unless defined $class;
#warn "no namespace part of the param" unless defined $namespaces;
my @objectdefs;
if ( ref $class eq 'ARRAY' ) { # collection
$message .= "<Collection>\n";
@objectdefs = $class;
}
else { # Nipple
@objectdefs = ($param);
}
foreach my $objectdef (@objectdefs) {
$message .= "<Simple>\n";
my ( $type, $Namespaces ) = @{$objectdef};
die "type is missing from objectdef " unless $type;
$message .= "<objectType>$type</objectType>\n";
if ( defined($Namespaces)
&& ( ref($Namespaces) ne 'ARRAY' ) )
{
return (
undef,
$self->errorRegXML(
"invalid structure of $inout namespaces for object $type; expected arrayref"
)
);
}
foreach my $ns ( @{$Namespaces} ) {
next unless $ns;
$message .= "<Namespace>$ns</Namespace>\n";
}
$message .= "</Simple>\n";
}
if ( ref($class) eq 'ARRAY' ) {
$message .= "</Collection>\n";
}
}
$message .= "</${inout}></${inout_lc}Objects>\n";
}
$message .= "</findService>\n";
# my $return = $self->SOAP_connection($reg)->call('findService' => ($message))->paramsall;
my ($return) = $self->_call( $reg, 'findService', $message );
return ( $self->_parseServices( $reg, $return ), undef );
}
=head2 retrieveService
Usage : $WSDL = $MOBY->retrieveService($ServiceInstance)
Function : get the WSDL definition of the service with this name/authority URI
Returns : a WSDL string
Args : The ServiceInstance object for that service (from findService call)
=cut
sub retrieveService {
my ( $self, $SI ) = @_;
return undef unless $SI && $SI->isa('MOBY::Client::ServiceInstance');
my $auth = $SI->authority;
my $name = $SI->name;
my $reg = $SI->registry;
return undef unless ( $auth && $name && $self->Connection($reg) );
my $message = "
<retrieveService>
" . ( $SI->XML ) . "
</retrieveService>";
my ($return) = $self->_call( $reg, 'retrieveService', $message );
my $parser = XML::LibXML->new();
my $doc = $parser->parse_string($return);
my $de = $doc->getDocumentElement;
my @child = $de->childNodes;
my $content;
foreach (@child) {
$debug && &_LOG( getNodeTypeName($_), "\t", $_->toString, "\n" );
if ( $_->nodeType == TEXT_NODE ) {
$content .= $_->nodeValue; #else try $_->textContent
}
else {
$content .= $_->toString;
}
}
$content =~ s/^\n//gs;
$content =~ s/<!\[CDATA\[((?>[^\]]+))\]\]>/$1/gs;
return $content;
}
=head2 retrieveResourceURLs
Usage : $names = $MOBY->retrieveResourceURLs()
Function : get a hash of the URL's for each of the MOBY ontologies
Returns : hashref to the following hash
$names{Ontology} = [URL1, URL2,...]
Args : none
=cut
sub retrieveResourceURLs {
my ($self, %args) = shift;
my $reg = $args{registry};
$reg = $reg ? $reg : $self->default_MOBY_servername;
return undef unless ( $self->Connection($reg) );
my ($return) = $self->_call( $reg, 'retrieveResourceURLs', "" );
my $parser = XML::LibXML->new();
my $doc = $parser->parse_string($return);
my $root = $doc->getDocumentElement;
my $urls_list = $root->childNodes;
my %urls;
for ( my $x = 1 ; $x <= $urls_list->size() ; $x++ ) {
next unless $urls_list->get_node($x)->nodeType == ELEMENT_NODE;
my $ontology = $urls_list->get_node($x)->getAttributeNode('name')->getValue;
my $url = $urls_list->get_node($x)->getAttributeNode('url')->getValue;
push @{ $urls{$ontology} }, $url
}
return \%urls;
}
=head2 retrieveServiceNames
Usage : $names = $MOBY->retrieveServiceNames(%args)
Function : get a (redundant) list of all registered service names
(N.B. NOT service types!)
Returns : hashref to the following hash
$names{$AuthURI} = [serviceName_1, serviceName_2, serviceName3...]
Args : registry => $reg_name: name of registry you wish to retrieve from (optional)
as_lsid => $boolean: return service names as their corresponding LSID's (default off)
=cut
sub retrieveServiceNames {
my ($self, %args) = @_;
my $reg = $args{registry};
my $aslsid = $args{as_lsid};
$reg = $reg ? $reg : $self->default_MOBY_servername;
return undef unless ( $self->Connection($reg) );
# my $return = $self->SOAP_connection($reg)->call('retrieveServiceNames' => (@_))->paramsall;
my ($return) = $self->_call( $reg, 'retrieveServiceNames', "" );
my $parser = XML::LibXML->new();
my $doc = $parser->parse_string($return);
my $root = $doc->getDocumentElement;
my $names_list = $root->childNodes;
my %servicenames;
for ( my $x = 1 ; $x <= $names_list->size() ; $x++ ) {
next unless $names_list->get_node($x)->nodeType == ELEMENT_NODE;
my $name =
$names_list->get_node($x)->getAttributeNode('name')->getValue;
my $auth =
$names_list->get_node($x)->getAttributeNode('authURI')->getValue;
my $lsid = $names_list->get_node($x)->getAttributeNode('lsid');
if ($lsid){
$lsid = $lsid->getValue;
} else {
$lsid = $name;
}
$lsid ||=$name;
push @{ $servicenames{$auth} }, $aslsid?$lsid:$name;
}
return \%servicenames;
}
=head2 retrieveServiceProviders
Usage : @URIs = $MOBY->retrieveServiceProviders([$reg_name])
Function : get the list of all provider's AuthURI's
Returns : list of service provider URI strings
Args : $reg_name: name of registry you wish to retrieve from (optional)
=cut
sub retrieveServiceProviders {
my ($self) = shift;
my $reg = shift;
$reg = $reg ? $reg : $self->default_MOBY_servername;
return undef unless ( $self->Connection($reg) );
# my $return = $self->SOAP_connection($reg)->call('retrieveServiceProviders' => (@_))->paramsall;
my ($return) = $self->_call( $reg, 'retrieveServiceProviders', "" );
my $parser = XML::LibXML->new();
my $doc = $parser->parse_string($return);
my $root = $doc->getDocumentElement;
my $providers = $root->childNodes;
my @serviceproviders;
for ( my $x = 1 ; $x <= $providers->size() ; $x++ ) {
next unless $providers->get_node($x)->nodeType == ELEMENT_NODE;
push @serviceproviders,
$providers->get_node($x)->getAttributeNode('name')->getValue;
}
return @serviceproviders;
}
=head2 retrieveServiceTypes
Usage : $types = $MOBY->retrieveServiceTypes(%args)
Function : get the list of all registered service types
Returns : hashref of $types{$type} = $definition
Args : registry => $reg_name: name of registry you wish to retrieve from (optional)
as_lsid => $boolean: return the $type as its corresponding LSID (defualt off)
=cut
sub retrieveServiceTypes {
my ($self, %args) = shift;
my $reg = $args{registry};
my $as_lsid = $args{as_lsid};
$reg = $reg ? $reg : $self->default_MOBY_servername;
return undef unless ( $self->Connection($reg) );
# my $return = $self->SOAP_connection($reg)->call('retrieveServiceTypes' => (@_))->paramsall;
my ($return) = $self->_call( $reg, 'retrieveServiceTypes', "" );
my $parser = XML::LibXML->new();
my $doc = $parser->parse_string($return);
my $root = $doc->getDocumentElement;
my $types = $root->childNodes;
my %servicetypes;
for ( my $x = 1 ; $x <= $types->size() ; $x++ ) {
next unless $types->get_node($x)->nodeType == ELEMENT_NODE;
my $type = $types->get_node($x)->getAttributeNode('name')->getValue;
my $lsid = $types->get_node($x)->getAttributeNode('lsid');
if ($lsid){
$lsid = $lsid->getValue;
} else {
$lsid = $type;
}
my $desc;
for
my $elem ( $types->get_node($x)->getElementsByTagName('Description') )
{
$desc = $elem->firstChild->toString;
if ( $desc =~ /<!\[CDATA\[((?>[^\]]+))\]\]>/ ) {
$desc = $1;
}
}
$desc =~ s/<!\[CDATA\[((?>[^\]]+))\]\]>/$1/gs;
$servicetypes{$as_lsid?$lsid:$type} = $desc;
}
return \%servicetypes;
}
=head2 retrieveServiceTypesFull
Usage : $types = $MOBY->retrieveServiceTypesFull(%args)
Function : get all details of all service types
Returns : hashref of $types{$type} = {Description => "definition",
authURI => "authority.uri.here",
contactEmail => "email@addy.here",
ISA => "parentType", # possibly empty string ""
ISA_LSID => "urn:lsid...parentLSID"} # possibly empty string ""
Args : registry => $reg_name: name of registry you wish to retrieve from (optional)
as_lsid => $boolean: return the $type as its corresponding LSID (defualt off)
=cut
sub retrieveServiceTypesFull {
my ($self, %args) = shift;
my $reg = $args{registry};
my $as_lsid = $args{as_lsid};
$reg = $reg ? $reg : $self->default_MOBY_servername;
return undef unless ( $self->Connection($reg) );
# my $return = $self->SOAP_connection($reg)->call('retrieveServiceTypes' => (@_))->paramsall;
my ($return) = $self->_call( $reg, 'retrieveServiceTypes', "" );
my $parser = XML::LibXML->new();
my $doc = $parser->parse_string($return);
my $root = $doc->getDocumentElement;
my $types = $root->childNodes;
my %servicetypes;
for ( my $x = 1 ; $x <= $types->size() ; $x++ ) {
next unless $types->get_node($x)->nodeType == ELEMENT_NODE;
my $type = $types->get_node($x)->getAttributeNode('name')->getValue;
my $lsid = $types->get_node($x)->getAttributeNode('lsid');
if ($lsid){
$lsid = $lsid->getValue;
} else {
$lsid = $type;
}
my ($desc, $auth, $email, $ISA, $ISA_LSID) = ("","","","","");
for
my $elem ( $types->get_node($x)->getElementsByTagName('Description') )
{
$desc = $elem->firstChild->toString;
if ( $desc =~ /<!\[CDATA\[((?>[^\]]+))\]\]>/ ) {
$desc = $1;
}
}
for
my $elem ( $types->get_node($x)->getElementsByTagName('authURI') )
{
$auth = $elem->firstChild->toString;
if ( $auth =~ /<!\[CDATA\[((?>[^\]]+))\]\]>/ ) {
$auth = $1;
}
}
for
my $elem ( $types->get_node($x)->getElementsByTagName('contactEmail') )
{
$email = $elem->firstChild->toString;
if ( $email =~ /<!\[CDATA\[((?>[^\]]+))\]\]>/ ) {
$email = $1;
}
}
for
my $elem ( $types->get_node($x)->getElementsByTagName('ISA') )
{
$ISA = $elem->firstChild;
$ISA = $ISA?$ISA->toString:"";
if ( $email =~ /<!\[CDATA\[((?>[^\]]+))\]\]>/ ) {
$email = $1;
}
$ISA_LSID = $elem->getAttributeNode('lsid')->getValue;
}
$desc =~ s/<!\[CDATA\[((?>[^\]]+))\]\]>/$1/gs; # somehow these CDATA elements are nested sometimes???
$servicetypes{$as_lsid?$lsid:$type} = {Description => $desc, authURI => $auth, contactEmail => $email, ISA => $ISA, ISA_LSID => $ISA_LSID};
}
return \%servicetypes;
}
=head2 retrieveObjectNames
Usage : $names = $MOBY->retrieveObjectNames(%args)
Function : get the list of all registered Object types
Returns : hashref of hash:
$names{$name} = $definition
Args : registry => $reg_name: name of registry you wish to retrieve from (optional)
as_lsid => $boolean: return $name as its correspnding LSID (optional default off)
=cut
sub retrieveObjectNames {
my ($self, %args) = @_;
my $reg = $args{registry};
my $as_lsid = $args{as_lsid};
$reg = $reg ? $reg : $self->default_MOBY_servername;
return undef unless ( $self->Connection($reg) );
my ($return) = $self->_call( $reg, 'retrieveObjectNames', "" );
my $parser = XML::LibXML->new();
my $doc = $parser->parse_string($return);
my $root = $doc->getDocumentElement;
my $obnames = $root->childNodes;
my %objectnames;
for ( my $x = 1 ; $x <= $obnames->size() ; $x++ ) {
next unless $obnames->get_node($x)->nodeType == ELEMENT_NODE;
my $name = $obnames->get_node($x)->getAttributeNode('name')->getValue;
my $lsid = $obnames->get_node($x)->getAttributeNode('lsid');
if ($lsid){
$lsid = $lsid->getValue;
} else {
$lsid = $name;
}
my $desc;
for my $elem (
$obnames->get_node($x)->getElementsByTagName('Description') )
{
$desc = $elem->firstChild->toString;
if ( $desc =~ /<!\[CDATA\[((?>[^\]]+))\]\]>/ ) {
$desc = $1;
}
}
$desc =~ s/<!\[CDATA\[((?>[^\]]+))\]\]>/$1/gs;
$objectnames{$as_lsid?$lsid:$name} = $desc;
}
return \%objectnames;
}
=head2 retrieveObjectDefinition
Usage : $DEF = $MOBY->retrieveObjectDefinition(objectType => $objectType)
Function : retrieve the $XML that was used to register an object and its relationships
Returns : hashref, identical to the hash sent during Object registration, plus
an additional XML hash key that contains the actual XML containing
the object definition as sent by MOBY Central (used for a visual
overview, rather than parsing all of the hash keys)
objectType => "the name of the Object"
objectLSID => "urn:lsid:..."
description => "a human-readable description of the object"
contactEmail => "your@email.address"
authURI => "URI of the registrar of this object"
Relationships => {
relationshipType1 => [
{object => Object1,
articleName => ArticleName1,
lsid => lsid1},
{object => Object2,
articleName => ArticleName2,
lsid => lsid2}
],
relationshipType2 => [
{object => Object3,
articleName => ArticleName3,
lsid => lsid3}
]
}
XML => <....XML of object registration.../>
Args : objectType => the name or LSID URI for an object
=cut
sub retrieveObjectDefinition {
my ( $self, %a ) = @_;
my $id = $a{objectType};
return $self->errorRegXML(
"Function not allowed when querying multiple registries")
if $self->multiple_registries;
my %def;
return \%def unless $id;
my $message = "
<retrieveObjectDefinition>
<objectType>$id</objectType>
</retrieveObjectDefinition>";
my ($return) =
$self->_call( 'default', 'retrieveObjectDefinition', $message );
return \%def unless $return;
my ( $term, $lsid, $desc, $relationships, $email, $authURI ) =
&_ObjectDefinitionPayload($return);
$def{objectType} = $term;
$def{objectLSID} = $lsid;
$def{description} = $desc;
$def{contactEmail} = $email;
$def{authURI} = $authURI;
$def{Relationships} = $relationships;
$def{XML} = $return;
return ( \%def );
}
sub _ObjectDefinitionPayload {
my ($payload) = @_;
my $Parser = XML::LibXML->new();
my $doc = $Parser->parse_string($payload);
my $Object = $doc->getDocumentElement();
my $obj = $Object->nodeName;
return undef unless ( $obj eq 'retrieveObjectDefinition' );
my $term = &_nodeTextContent( $Object, "objectType" );
my $lsid = &_nodeAttributeValue( $Object, "objectType", "lsid");
my $desc = &_nodeCDATAContent( $Object, "Description" );
if ( $desc =~ /<!\[CDATA\[((?>[^\]]+))\]\]>/ ) {
$desc = $1;
}
my $authURI = &_nodeTextContent( $Object, "authURI" );
my $email = &_nodeTextContent( $Object, "contactEmail" );
my %att_value;
my %relationships;
my $x = $doc->getElementsByTagName("Relationship");
my $no_relationships = $x->size();
for ( my $n = 1 ; $n <= $no_relationships ; ++$n ) { #get_node starts at one
my $relationshipType =
$x->get_node($n)->getAttributeNode('relationshipType')
; # may or may not have a name
if ($relationshipType) {
$relationshipType = $relationshipType->getValue();
}
else {
return
"FAILED! must include a relationshipType in every relationship\n";
}
my @child = $x->get_node($n)->childNodes;
foreach (@child) {
next unless $_->nodeType == ELEMENT_NODE;
my $article =
$_->getAttributeNode('articleName'); # may or may not have a name
my $rlsid =
$_->getAttributeNode('lsid'); # may or may not have a name
if ($article) { $article = $article->getValue() }
if ($rlsid) { $rlsid = $rlsid->getValue() }
my @child2 = $_->childNodes;
foreach (@child2) {
#print getNodeTypeName($_), "\t", $_->toString,"\n";
next unless $_->nodeType == TEXT_NODE;
push @{ $relationships{$relationshipType} },
{ object => $_->toString,
articleName => $article,
lsid => $rlsid };
}
}
}
return ( $term, $lsid, $desc, \%relationships, $email, $authURI );
}
=head2 retrieveNamespaces
Usage : $ns = $MOBY->retrieveNamespaces(%args)
Function : get the list of all registered Namespace types
Returns : hashref of hash:
$ns{$namespace} = $definition
Args : registry => $reg_name: name of registry you wish to retrieve from (optional)
as_lsid => $boolean: retrieve $namespace as its corresponding LSID (default off)
=cut
sub retrieveNamespaces {
my ($self, %args) = shift;
my $reg = $args{registry};
$reg = $reg ? $reg : $self->default_MOBY_servername;
return undef unless ( $self->Connection($reg) );
my $as_lsid = $args{as_lsid};
my ($return) = $self->_call( $reg, 'retrieveNamespaces', "" );
my $parser = XML::LibXML->new();
my $doc = $parser->parse_string($return);
my $root = $doc->getDocumentElement;
my $namesp = $root->childNodes;
my %namespaces;
for ( my $x = 1 ; $x <= $namesp->size() ; $x++ ) {
next unless $namesp->get_node($x)->nodeType == ELEMENT_NODE;
my $ns = $namesp->get_node($x)->getAttributeNode('name')->getValue;
my $lsid = $namesp->get_node($x)->getAttributeNode('lsid');
if ($lsid){
$lsid = $lsid->getValue;
} else {
$lsid = $ns;
}
my $desc;
for my $elem (
$namesp->get_node($x)->getElementsByTagName('Description') )
{
$desc = $elem->firstChild;
$desc = $desc ? $desc->toString : "";
$desc ||="";
if ( $desc =~ /<!\[CDATA\[((?>[^\]]+))\]\]>/ ) {
$desc = $1;
}
}
# $desc =~ s/<!\[CDATA\[((?>[^\]]+))\]\]>/$1/gs;
$namespaces{$as_lsid?$lsid:$ns} = $desc;
}
return \%namespaces;
}
=head2 retrieveNamespacesFull
Usage : $ns = $MOBY->retrieveNamespaces(%args)
Function : get all details about all namespaces
Returns : hashref of hash:
$ns{$namespace} = {Definition => $definition,
authURI => $authority,
contactEmail => $email}
Args : registry => $reg_name: name of registry you wish to retrieve from (optional)
as_lsid => $boolean: retrieve $namespace as its corresponding LSID (default off)
=cut
sub retrieveNamespacesFull {
my ($self, %args) = shift;
my $reg = $args{registry};
$reg = $reg ? $reg : $self->default_MOBY_servername;
return undef unless ( $self->Connection($reg) );
my $as_lsid = $args{as_lsid};
my ($return) = $self->_call( $reg, 'retrieveNamespaces', "" );
my $parser = XML::LibXML->new();
my $doc = $parser->parse_string($return);
my $root = $doc->getDocumentElement;
my $namesp = $root->childNodes;
my %namespaces;
for ( my $x = 1 ; $x <= $namesp->size() ; $x++ ) {
next unless $namesp->get_node($x)->nodeType == ELEMENT_NODE;
my $ns = $namesp->get_node($x)->getAttributeNode('name')->getValue;
my $lsid = $namesp->get_node($x)->getAttributeNode('lsid');
if ($lsid){
$lsid = $lsid->getValue;
} else {
$lsid = $ns;
}
my ($desc, $auth, $email);
for my $elem (
$namesp->get_node($x)->getElementsByTagName('Description') )
{
$desc = $elem->firstChild;
$desc = $desc ? $desc->toString : "";
$desc ||="";
if ( $desc =~ /<!\[CDATA\[((?>[^\]]+))\]\]>/ ) {
$desc = $1;
}
}
for my $elem (
$namesp->get_node($x)->getElementsByTagName('authURI') )
{
$auth = $elem->firstChild;
$auth = $auth ? $auth->toString : "";
$auth ||="";
if ( $auth =~ /<!\[CDATA\[((?>[^\]]+))\]\]>/ ) {
$auth = $1;
}
}
for my $elem (
$namesp->get_node($x)->getElementsByTagName('contactEmail') )
{
$email = $elem->firstChild;
$email = $email ? $email->toString : "";
$email ||="";
if ( $email =~ /<!\[CDATA\[((?>[^\]]+))\]\]>/ ) {
$email = $1;
}
}
$namespaces{$as_lsid?$lsid:$ns} = {Description => $desc, authURI => $auth, contactEmail => $email};
}
return \%namespaces;
}
=head2 retrieveObject
Usage : $objects = $MOBY->retrieveObjectNames(%args)
Function : get the object xsd
Returns : hashref of hash:
$objects{$name} = $W3C_XML_Schema_string
Args : registry => $reg - name of MOBY Central you want to use (must pass undef otherwise)
objectType => $name - object name (from ontology) or undef to get all objects
as_lsid => $boolean - return $name as its corresponding LSID (default off)
=cut
sub retrieveObject {
my ($self, %args) = shift;
my ($reg) = $args{registry};
my $type = $args{objectType};
my $as_lsid = $args{as_lsid};
my $message = "
<retrieveObject>
<objectType>$type</objectType>
</retrieveObject>";
$reg = $reg ? $reg : $self->default_MOBY_servername;
return undef unless ( $self->Connection($reg) );
my ($return) = $self->_call( $reg, 'retrieveObject', $message );
my $parser = XML::LibXML->new();
my $doc = $parser->parse_string($return);
my $root = $doc->getDocumentElement;
my $objects = $root->childNodes;
my %objects;
for ( my $x = 1 ; $x <= $objects->size() ; $x++ ) {
next unless $objects->get_node($x)->nodeType == ELEMENT_NODE;
my $name = $objects->get_node($x)->getAttributeNode('name')->getValue;
my $lsid = $objects->get_node($x)->getAttributeNode('lsid');
if ($lsid){
$lsid = $lsid->getValue;
} else {
$lsid = $name;
}
my $desc;
for my $elem ( $objects->get_node($x)->getElementsByTagName('Schema') )
{
$desc = $elem->firstChild->nodeValue;
if ( $desc =~ /<!\[CDATA\[((?>[^\]]+))\]\]>/ ) {
$desc = $1;
}
}
$desc =~ s/<!\[CDATA\[((?>[^\]]+))\]\]>/$1/gs;
$objects{$name} = $desc;
}
return \%objects;
}
=head2 Relationships
Usage : $def = $MOBY->Relationships(%args)
Function : traverse and return the relationships in the ontology
Returns : hashref of
FOR SERVICES:
$hash{'isa'}=[{lsid => $lsid, term => 'termy'},...]
FOR OBJECTS:
$hash{relationship_type}=[{lsid => $lsid, articleName => 'thingy', term => 'termy'},...]
Args : EITHER serviceType => $term_or_lsid
OR objectType => $term_or_lsid
Relationships => \@relationship_types (optional, 'all' if parameter is missing)
Registry => $registry_name (optional)
expandRelationships => [1/0] (optional)
direction => ['root'/'leaves'] (optional)
=cut
sub Relationships {
my ( $self, %args ) = @_;
my $object = $args{'objectType'};
my $service = $args{'serviceType'};
my $expand = $args{'expandRelationships'};
$expand = $args{'expandRelationship'}
unless defined($expand); # be forgiving of typos
my $direction = $args{'direction'} ?
$args{'direction'} :
'root'; # make 'root' default to stay compatible
my @relationships;
@relationships = @{ $args{'Relationships'} }
if ( $args{'Relationships'}
&& ( ref( $args{'Relationships'} ) eq 'ARRAY' ) );
push @relationships, 'isa' unless $relationships[0]; # need to have at least one relationship
my $reg = $args{'Registry'};
my $m;
my $payload;
return {} unless ( $object || $service );
if ($object) {
$m = "
<Relationships>
<objectType>$object</objectType>\n";
foreach (@relationships) {
$m .= "<relationshipType>$_</relationshipType>\n";
}
$m .= "<expandRelationship>1</expandRelationship>\n" if $expand;
$m .= "<direction>$direction</direction>\n";
$m .= "</Relationships>";
$reg = $reg ? $reg : $self->default_MOBY_servername;
return undef unless ( $self->Connection($reg) );
#$payload = $self->SOAP_connection($reg)->call('Relationships' => ($m))->paramsall;
($payload) = $self->_call( $reg, 'Relationships', $m );
}
elsif ($service) {
$m = "
<Relationships>
<serviceType>$service</serviceType>\n";
foreach (@relationships) {
$m .= "<relationshipType>$_</relationshipType>\n";
}
$m .= "<expandRelationship>1</expandRelationship>\n" if $expand;
$m .= "<direction>$direction</direction>\n";
$m .= "</Relationships>";
$reg = $reg ? $reg : $self->default_MOBY_servername;
return undef unless ( $self->Connection($reg) );
# $payload = $self->SOAP_connection($reg)->call('Relationships' => ($m))->paramsall;
($payload) = $self->_call( $reg, 'Relationships', $m );
}
return &_relationshipsPayload($payload);
}
sub _relationshipsPayload {
my ($payload) = @_;
return undef unless $payload;
my %att_value;
my %relationships;
my $Parser = XML::LibXML->new();
my $doc = $Parser->parse_string($payload);
my $x = $doc->getElementsByTagName("Relationship");
my $no_relationships = $x->size();
for ( my $n = 1 ; $n <= $no_relationships ; ++$n ) {
my $relationshipType = $x->get_node($n)->getAttributeNode('relationshipType'); # may or may not have a name
if ($relationshipType) {
$relationshipType = $relationshipType->getValue();
} else {
return "FAILED! must include a relationshipType in every relationship\n";
}
my @child = $x->get_node($n)->childNodes;
foreach my $child(@child) {
my ($lsid, $article, $term) = ("", "", "");
next unless $child->nodeType == ELEMENT_NODE;
my $lsidattr = $child->getAttributeNode('lsid'); # may or may not have a name
if ($lsidattr) {
$lsid = $lsidattr->getValue();
}
my $ARTattr = $child->getAttributeNode('articleName'); # may or may not have a name
if ($ARTattr) {
$article = $ARTattr->getValue();
}
my %info;
$info{lsid} = $lsid;
($info{articleName} = $article) if $article;
my @child2 = $child->childNodes;
foreach my $child2(@child2) {
next unless $child2->nodeType == TEXT_NODE;
$info{term} = $child2->toString;
push @{ $relationships{$relationshipType} }, \%info;
}
}
}
return \%relationships;
}
=head2 ISA
Usage : $def = $MOBY->ISA($class1, $class2)
Function : a pre-canned use of the Relationships function
to quickly get an answer to whether class1 ISA class2
Returns : Boolean
Args : $class1 - an Object ontology term or LSID
$class2 - an Object ontology term or LSID
=cut
sub ISA {
my ( $self, $class1, $class2 ) = @_;
return 1
if ( ( $class1 eq $class2 )
|| ( "moby:$class1" eq $class2 )
|| ( $class1 eq "moby:$class2" ) );
my $lsid1 = $self->ObjLSID($class1);
my $lsid2 = $self->ObjLSID($class2);
return 0 unless $lsid1 && $lsid2;
my @lsids;
unless ( @lsids = $self->ISA_CACHE($lsid1) ) {
my $resp = $self->Relationships(
objectType => $lsid1,
expandRelationship => 1,
Relationships => ['isa']
);
my $lsids = $resp->{'isa'};
map {push @lsids, $self->ObjLSID($_->{lsid})} @$lsids; # convert to LSID
$self->ISA_CACHE( $lsid1, [@lsids] );
$self->ISA_CACHE( $class1, [@lsids] );
my @hold = @lsids;
while ( shift @hold ) {
$self->ISA_CACHE( $_, [@hold] );
if ( $_ =~ /^urn:lsid:biomoby.org.\w+\.(\S+)/ ) {
$self->ISA_CACHE( $1, [@lsids] );
}
}
}
foreach (@lsids) {
return 1 if $_ eq $lsid2;
}
return 0;
}
=head2 DUMP
Usage : ($mobycentral, $mobyobject, $mobyservice, $mobynamespace, $mobyrelationship) = $MOBY->DUMP(['registry'])
Function : DUMP the mysql for the current MOBY Central database
Returns : text
Args : $reg - name of MOBY Central you want to use if not default
=cut
sub DUMP {
my ($self) = shift;
my ($reg) = shift;
my $type = shift;
$reg = $reg ? $reg : $self->default_MOBY_servername;
return undef unless ( $self->Connection($reg) );
# return $self->SOAP_connection($reg)->call('DUMP')->paramsall;
my ($SQLs) = $self->_call( $reg, 'DUMP_MySQL', "" );
my (
$mobycentral, $mobyobject, $mobyservice,
$mobynamespace, $mobyrelationship
) = @{$SQLs} unless ref($SQLs) eq 'HASH';
# cases where soap message is serialized as a HASH
(
$mobycentral, $mobyobject, $mobyservice,
$mobynamespace, $mobyrelationship
) = @{$SQLs->{item}} if ref($SQLs) eq 'HASH';
return (
$mobycentral, $mobyobject, $mobyservice,
$mobynamespace, $mobyrelationship
);
}
*DUMP_MySQL = \&DUMP;
*DUMP_MySQL = \&DUMP;
sub _parseServices {
my ( $self, $Registry, $XML ) = @_;
my $Parser = XML::LibXML->new();
# fix empty string problem
return [] unless $XML;
my $doc = $Parser->parse_string($XML);
my $Object = $doc->getDocumentElement();
my $Services = $Object->getElementsByTagName("Service");
my $num = $Services->size();
my @Services;
for ( my $x = 1 ; $x <= $num ; $x++ ) {
my $Service = $Services->get_node($x);
my $AuthURI = $Service->getAttributeNode('authURI')->getValue;
my $servicename = $Service->getAttributeNode('serviceName')->getValue;
my $lsid = $Service->getAttributeNode('lsid');
if ($lsid){
$lsid = $lsid->getValue;
} else {
$lsid = "";
}
my $Type = &_nodeTextContent( $Service, 'serviceType' );
my $signatureURL = &_nodeTextContent( $Service, 'signatureURL' );
my $authoritative = &_nodeTextContent( $Service, 'authoritative' );
my $contactEmail = &_nodeTextContent( $Service, 'contactEmail' );
my $URL = &_nodeTextContent( $Service, 'URL' );
#my $Output = &_nodeTextContent($Service, 'outputObject');
my $Description = &_nodeCDATAContent( $Service, 'Description' );
$Description =~ s/<!\[CDATA\[((?>[^\]]+))\]\]>/$1/gs;
my $cat = &_nodeTextContent( $Service, 'Category' );
my @INPUTS;
my @OUTPUTS;
foreach my $inout ( "Input", "Output" ) {
my $xPuts =
$Service->getElementsByTagName($inout)
; # there should only be one, but... who knows what
for my $in ( 1 .. $xPuts->size() ) {
my $current = $xPuts->get_node($in);
foreach my $child ( $current->childNodes )
{ # child nodes will be either "Simple" or "Collection" tagnames
next unless $child->nodeType == ELEMENT_NODE;
my $THIS;
if ( $child->nodeName eq "Simple" ) {
$THIS =
MOBY::Client::SimpleArticle->new( XML_DOM => $child );
}
elsif ( $child->nodeName eq "Collection" ) {
$THIS =
MOBY::Client::CollectionArticle->new(
XML_DOM => $child );
}
else {
next;
}
if ( $inout eq "Input" ) {
push @INPUTS, $THIS;
}
else {
push @OUTPUTS, $THIS;
}
}
}
}
my @SECONDARIES;
my $secs =
$Service->getElementsByTagName("secondaryArticles")
; # there should only be one, but... who knows what
for my $in ( 1 .. $secs->size() ) {
my $current = $secs->get_node($in);
foreach my $param ( $current->childNodes )
{ # child nodes will be "Parameter" tag names
next
unless $param->nodeType == ELEMENT_NODE
&& $param->nodeName eq "Parameter";
my $THIS;
$THIS =
MOBY::Client::SecondaryArticle->new( XML_DOM => $param );
push @SECONDARIES, $THIS;
}
}
my $Instance = MOBY::Client::ServiceInstance->new(
authority => $AuthURI,
authoritative => $authoritative,
URL => $URL,
LSID => $lsid,
contactEmail => $contactEmail,
name => $servicename,
type => $Type,
category => $cat,
input => \@INPUTS,
output => \@OUTPUTS,
secondary => \@SECONDARIES,
description => $Description,
registry => $Registry,
signatureURL => $signatureURL,
XML => $Service->toString,
);
push @Services, $Instance;
}
return \@Services;
}
# my ($e, $m, $lsid) = $OS->objectExists(term => $_);
=head2 ObjLSID
=cut
sub ObjLSID {
my ( $self, $term ) = @_;
return undef unless $term;
my $lsid;
if ( $lsid = $self->LSID_CACHE($term) ) {
return $lsid;
}
else {
my $os = MOBY::Client::OntologyServer->new;
my ( $s, $m, $tlsid ) = $os->objectExists( term => $term );
if ($tlsid) {
$self->LSID_CACHE( $term, $tlsid ); # link both the term
$self->LSID_CACHE( $tlsid, $tlsid ); # and the lsid to itself
return $tlsid;
}
else {
return undef;
}
}
}
=head2 LSID_CACHE
Usage : $lsid = $MOBY->LSID_CACHE($term, $lsid)
Function : get/set LSID from the cache
Returns : lsid as a scalar
Args : the term for which you have/want an lsid,
and optionally the lsid to set.
=cut
sub LSID_CACHE {
my ( $self, $term, $lsid ) = @_;
if ( $term && $lsid ) {
$self->{LSID_CACHE}->{$term} = $lsid;
return $self->{LSID_CACHE}->{$term};
}
elsif ($term) {
return $self->{LSID_CACHE}->{$term};
}
else {
return undef;
}
}
=head2 ISA_CACHE
Usage : @lsids = $MOBY->ISA_CACHE($lsid, \@isas)
Function : get/set the ISA relationships in the cache
Returns : list of ISA relationships. The ISA list
is IN ORDER from, excluding the term itself, to
root Object. Base Object returns an empty list.
Args : The LSID for which you have/want the ISA parentage,
and optionally the parentage listref to set.
Note : WHAT COMES BACK ARE LSIDs!!!
=cut
sub ISA_CACHE {
my ( $self, $desiredterm, $isas ) = @_;
my $term = $desiredterm;
return (undef) if $isas && ( ref($isas) ne 'ARRAY');
if ( $term && $isas ) {
my @isalsids;
foreach (@$isas){
my $lsid = $self->ObjLSID($_);
next unless ($lsid =~ /^urn\:lsid/);
push @isalsids, $lsid;
}
$self->{ISA_CACHE}->{$desiredterm} = [(@isalsids)]; # can't assign a listreference or it will empty itself!
while ( my $term = shift(@isalsids) ) { # traverse down and flatten the list
$self->{ISA_CACHE}->{$term} = [(@isalsids)];
}
return @{ $self->{ISA_CACHE}->{$desiredterm} };
}
elsif ( $term && $self->{ISA_CACHE}->{$desiredterm} ) {
return @{ $self->{ISA_CACHE}->{$desiredterm} };
}
else {
return ();
}
}
sub parseRegXML {
#<MOBYRegistration>
# <id>$id</id>
# <success>$success</success>
# <message><![CDATA[$message]]></message>
#</MOBYRegistration>
my ( $self, $xml ) = @_;
my $Parser = XML::LibXML->new();
#print STDERR $xml;
my $doc = $Parser->parse_string($xml);
my $Object = $doc->getDocumentElement();
my $obj = $Object->nodeName;
return undef unless ( $obj eq 'MOBYRegistration' );
my $id = &_nodeTextContent( $Object, 'id' );
my $success = &_nodeTextContent( $Object, 'success' );
my $message = &_nodeCDATAContent( $Object, 'message' );
#print STDERR "******$message******\n";
my $RDF = &_nodeRawContent( $Object, 'RDF' );
my $reg = MOBY::Client::Registration->new(
success => $success,
message => $message,
registration_id => $id,
RDF => $RDF,
id => $id
);
return $reg;
}
sub errorRegXML {
my ( $self, $message ) = @_;
my $reg = MOBY::Client::Registration->new(
success => 0,
message => $message,
registration_id => -1,
);
return $reg;
}
sub _nodeCDATAContent {
# will get text of **all** child $node from the given $DOM
# regardless of their depth!!
my ( $DOM, $node ) = @_;
my $x = $DOM->getElementsByTagName($node);
unless ( $x->get_node(1) ) { return }
my @child = $x->get_node(1)->childNodes;
my $content;
foreach (@child) {
#print getNodeTypeName($_), "\t", $_->toString,"\n";
next
unless ( ( $_->nodeType == TEXT_NODE )
|| ( $_->nodeType == CDATA_SECTION_NODE ) );
$content = $_->textContent;
}
$content ||= "";
$content =~ s/<!\[CDATA\[((?>[^\]]+))\]\]>/$1/gs;
return $content;
}
sub _nodeTextContent {
# will get text of **all** child $node from the given $DOM
# regardless of their depth!!
my ( $DOM, $node ) = @_;
my $x = $DOM->getElementsByTagName($node);
unless ( $x->get_node(1) ) { return }
my @child = $x->get_node(1)->childNodes;
my $content;
foreach (@child) {
#print getNodeTypeName($_), "\t", $_->toString,"\n";
next
unless ( ( $_->nodeType == TEXT_NODE )
|| ( $_->nodeType == CDATA_SECTION_NODE ) );
$content = $_->textContent;
}
return $content;
}
sub _nodeAttributeValue {
my ( $DOM, $node, $attr ) = @_;
return "" unless $attr;
my $x = $DOM->getElementsByTagName($node);
unless ( $x->get_node(1) ) { return "" }
my $n = $x->get_node(1);
my $nodemap = $n->attributes($attr); # XML::LibXML::NamedNodeMap - the worst documented (i.e. undocumented) piece of code ever written! You have to read the source to figure out the interface...
my $attrnode = $nodemap->getNamedItem($attr);
my $attrval = $attrnode?($attrnode->value):"";
return $attrval;
}
sub _nodeRawContent {
# will get XML of **all** child $node from the given $DOM
# regardless of their depth!!
my ( $DOM, $node ) = @_;
my $x = $DOM->getElementsByTagName($node);
unless ( $x->get_node(1) ) { return }
my @child = $x->get_node(1)->childNodes;
my $content;
foreach (@child) {
#print getNodeTypeName($_), "\t", $_->toString,"\n";
# next unless $_->nodeType == TEXT_NODE;
$content .= $_->toString;
}
return $content;
}
sub _nodeArrayContent {
# will get array content of all child $node from given $DOM
# regardless of depth!
my ( $DOM, $node ) = @_;
$debug && &_LOG( "_nodeArrayContext received DOM: ",
$DOM->toString, "\nsearching for node $node\n" );
my @result;
my $x = $DOM->getElementsByTagName($node);
my @child = $x->get_node(1)->childNodes;
foreach (@child) {
next unless $_->nodeType == ELEMENT_NODE;
my @child2 = $_->childNodes;
foreach (@child2) {
#print getNodeTypeName($_), "\t", $_->toString,"\n";
next
unless ( ( $_->nodeType == TEXT_NODE )
|| ( $_->nodeType == CDATA_SECTION_NODE ) );
push @result, $_->textContent;
}
}
return @result;
}
sub AUTOLOAD {
no strict "refs";
my ( $self, $newval ) = @_;
$AUTOLOAD =~ /.*::(\w+)/;
my $attr = $1;
if ( $self->_accessible( $attr, 'write' ) ) {
*{$AUTOLOAD} = sub {
if ( defined $_[1] ) { $_[0]->{$attr} = $_[1] }
return $_[0]->{$attr};
}; ### end of created subroutine
### this is called first time only
if ( defined $newval ) {
$self->{$attr} = $newval;
}
return $self->{$attr};
}
elsif ( $self->_accessible( $attr, 'read' ) ) {
*{$AUTOLOAD} = sub {
return $_[0]->{$attr};
}; ### end of created subroutine
return $self->{$attr};
}
# Must have been a mistake then...
croak "No such method: $AUTOLOAD";
}
sub DESTROY { }
sub _LOG {
return unless $debug;
open LOG, ">>/tmp/CentralLogOut.txt" or die "can't open logfile $!\n";
print LOG join "\n", @_;
print LOG "\n---\n";
close LOG;
}
1;