[MOBY-guts] biomoby commit
Eddie Kawas
kawas at dev.open-bio.org
Mon Nov 24 14:38:33 UTC 2008
kawas
Mon Nov 24 09:38:32 EST 2008
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies
In directory dev.open-bio.org:/tmp/cvs-serv10602/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies
Modified Files:
Services.pm
Log Message:
added unit test information to the RDF that is outputted by this module.
moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies Services.pm,1.8,1.9
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Services.pm,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Services.pm 2008/10/31 18:40:37 1.8
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Services.pm 2008/11/24 14:38:32 1.9
@@ -125,21 +125,21 @@
$self->{datatype_uri} = $CONF->{mobyobject}->{resourceURL} || '';
$self->{namespace_uri} = $CONF->{mobynamespace}->{resourceURL} || '';
} unless $args{endpoint};
-
+
# save the endpoint/namespace/uri if passed in
$self->{endpoint} = $args{endpoint} if $args{endpoint};
$self->{namespace} = $args{endpoint} if $args{namespace};
unless ( $self->{instance_uri} ) {
- my $moby = MOBY::Client::Central->new(
+ my $moby =
+ MOBY::Client::Central->new(
Registries => {
mobycentral => {
URL => $self->{endpoint},
URI => 'http://mobycentral.cbr.nrc.ca/MOBY/Central'
}
}
- )
- if $self->{endpoint};
+ ) if $self->{endpoint};
# otherwise use default one
$moby = MOBY::Client::Central->new() unless $self->{endpoint};
@@ -176,10 +176,13 @@
$self->{namespace_uri} = $self->{namespace_uri} . "/"
unless $self->{namespace_uri} =~ m/^.*(\/{1})$/;
$self->{datatype_uri} = $self->{datatype_uri} . "/"
- unless $self->{datatype_uri} =~ m/^.*(\/{1})$/;
+ unless $self->{datatype_uri} =~ m/^.*(\/{1})$/;
#set the isAlive path
- $self->{is_alive_path} = $CONF->{mobycentral}->{service_tester_path} if $ENV{MOBY_SERVER} and $self->{endpoint} and $ENV{MOBY_SERVER} eq $self->{endpoint};
+ $self->{is_alive_path} = $CONF->{mobycentral}->{service_tester_path}
+ if $ENV{MOBY_SERVER}
+ and $self->{endpoint}
+ and $ENV{MOBY_SERVER} eq $self->{endpoint};
# done
return $self;
@@ -208,20 +211,20 @@
my $authURI = $hash->{authURI} || '';
my $name = $hash->{serviceName} || '';
my $prettyPrint = $hash->{prettyPrint} ? $hash->{prettyPrint} : 'yes';
- my $addIsAlive = $hash->{isAlive} ? $hash->{isAlive} : 'yes';
- my $services = [];
+ my $addIsAlive = $hash->{isAlive} ? $hash->{isAlive} : 'yes';
+ my $services = [];
my $RegObject;
# use the passed in endpoint if applicable
- my $moby = MOBY::Client::Central->new(
+ my $moby =
+ MOBY::Client::Central->new(
Registries => {
mobycentral => {
URL => $self->{endpoint},
URI => 'http://mobycentral.cbr.nrc.ca/MOBY/Central'
}
}
- )
- if $self->{endpoint};
+ ) if $self->{endpoint};
# otherwise use default one
$moby = MOBY::Client::Central->new() unless $self->{endpoint};
@@ -230,7 +233,8 @@
( $services, $RegObject ) =
$moby->findService( authURI => $authURI, serviceName => $name );
- } else {
+ }
+ else {
my (@URIS) = $moby->retrieveServiceProviders();
foreach my $provider (@URIS) {
my ( $instances, $RegObject ) =
@@ -265,13 +269,13 @@
my $node_factory = new RDF::Core::NodeFactory();
foreach my $SI (@$services) {
+
# used for computing checksums
- my $service_name = $SI->name;
+ my $service_name = $SI->name;
my $service_authority = $SI->authority;
- my $resource =
- new RDF::Core::Resource( $self->{instance_uri},
- $SI->authority . "," . $SI->name );
+ my $resource = new RDF::Core::Resource( $self->{instance_uri},
+ $SI->authority . "," . $SI->name );
$model->addStmt(
new RDF::Core::Statement(
$resource,
@@ -329,14 +333,18 @@
new RDF::Core::Literal( $SI->name )
)
);
- eval{
+ eval {
do {
+
# add is alive information if necessary
- if ( $self->{is_alive_path} and -e $self->{is_alive_path} and -r $self->{is_alive_path} ."/isAliveStats.xml") {
+ if ( $self->{is_alive_path}
+ and -e $self->{is_alive_path}
+ and -r $self->{is_alive_path} . "/isAliveStats.xml" )
+ {
my $parser = XML::LibXML->new();
- my $doc =
+ my $doc =
$parser->parse_file(
- $self->{is_alive_path} . '/isAliveStats.xml' );
+ $self->{is_alive_path} . '/isAliveStats.xml' );
my $value = "true";
my $id = $SI->authority . "," . $SI->name;
my @nodelist = $doc->getElementsByTagName("service");
@@ -346,30 +354,41 @@
last;
}
$model->addStmt(
- new RDF::Core::Statement(
- $resource,
- $resource->new( MOBY::RDF::Predicates::FETA->isAlive ),
- new RDF::Core::Literal($value)
- )
+ new RDF::Core::Statement(
+ $resource,
+ $resource->new(
+ MOBY::RDF::Predicates::FETA->isAlive
+ ),
+ new RDF::Core::Literal($value)
+ )
);
- } else {
-
+ }
+ else {
+
# by default, state the service is alive ...
$model->addStmt(
- new RDF::Core::Statement(
- $resource,
- $resource->new( MOBY::RDF::Predicates::FETA->isAlive ),
- new RDF::Core::Literal('true')
- )
+ new RDF::Core::Statement(
+ $resource,
+ $resource->new(
+ MOBY::RDF::Predicates::FETA->isAlive
+ ),
+ new RDF::Core::Literal('true')
+ )
);
}
- } unless $addIsAlive =~ /no/i;
+ } unless $addIsAlive =~ /no/i;
};
+
# add the authoring statements
- my $bnode = new RDF::Core::Resource(
- $self->{instance_uri},
- md5_hex("$service_authority/$service_name/" . MOBY::RDF::Predicates::FETA->providedBy )
- ); #$node_factory->newResource;
+ my $bnode =
+ new RDF::Core::Resource(
+ $self->{instance_uri},
+ md5_hex(
+ "$service_authority/$service_name/"
+ . MOBY::RDF::Predicates::FETA
+ ->providedBy
+ )
+ ); #$node_factory->newResource;
$model->addStmt(
new RDF::Core::Statement(
$resource,
@@ -401,20 +420,25 @@
)
);
$model->addStmt(
- new RDF::Core::Statement(
- $bnode,
- $resource->new( MOBY::RDF::Predicates::RDF->type ),
- new RDF::Core::Resource(
- MOBY::RDF::Predicates::FETA->organisation
- )
- )
+ new RDF::Core::Statement(
+ $bnode,
+ $resource->new( MOBY::RDF::Predicates::RDF->type ),
+ new RDF::Core::Resource(
+ MOBY::RDF::Predicates::FETA->organisation
+ )
+ )
);
# add parameter statements
- my $operation = new RDF::Core::Resource(
- $self->{instance_uri},
- md5_hex("$service_authority/$service_name/" . MOBY::RDF::Predicates::FETA->hasOperation)
- ); # $node_factory->newResource;
+ my $operation =
+ new RDF::Core::Resource(
+ $self->{instance_uri},
+ md5_hex(
+ "$service_authority/$service_name/"
+ . MOBY::RDF::Predicates::FETA
+ ->hasOperation
+ )
+ ); # $node_factory->newResource;
$model->addStmt(
new RDF::Core::Statement(
$resource,
@@ -440,9 +464,12 @@
)
);
$bnode = new RDF::Core::Resource(
- $self->{instance_uri},
- md5_hex("$service_authority/$service_name/" . MOBY::RDF::Predicates::FETA->performsTask)
- ); # $node_factory->newResource;
+ $self->{instance_uri},
+ md5_hex(
+ "$service_authority/$service_name/"
+ . MOBY::RDF::Predicates::FETA->performsTask
+ )
+ ); # $node_factory->newResource;
$model->addStmt(
new RDF::Core::Statement(
$operation,
@@ -460,26 +487,107 @@
)
);
$model->addStmt(
- new RDF::Core::Statement(
- $bnode,
- $resource->new( MOBY::RDF::Predicates::RDF->type ),
- new RDF::Core::Resource(
- $self->{service_uri} . $SI->type
+ new RDF::Core::Statement(
+ $bnode,
+ $resource->new( MOBY::RDF::Predicates::RDF->type ),
+ new RDF::Core::Resource( $self->{service_uri} . $SI->type )
)
- )
);
+ # add unit test data here ...
+ if ( $SI->unitTest ) {
+ my $unit_test = $SI->unitTest;
+ $bnode =
+ new RDF::Core::Resource(
+ $self->{instance_uri},
+ md5_hex(
+ "$service_authority/$service_name/"
+ . MOBY::RDF::Predicates::FETA
+ ->unitTest
+ )
+ );
+
+ # add the type
+ $model->addStmt(
+ new RDF::Core::Statement(
+ $bnode,
+ $resource->new( MOBY::RDF::Predicates::RDF->type ),
+ new RDF::Core::Resource(
+ MOBY::RDF::Predicates::FETA->unitTest
+ )
+ )
+ );
+
+ # add the example input if defined
+ $model->addStmt(
+ new RDF::Core::Statement(
+ $bnode,
+ $resource->new( MOBY::RDF::Predicates::FETA->exampleInput ),
+ new RDF::Core::Literal( $unit_test->example_input )
+ )
+ )
+ if $unit_test->example_input
+ and $unit_test->example_input ne '';
+
+ # add the valid output xml if defined
+ $model->addStmt(
+ new RDF::Core::Statement(
+ $bnode,
+ $resource->new(
+ MOBY::RDF::Predicates::FETA->validOutputXML
+ ),
+ new RDF::Core::Literal( $unit_test->expected_output )
+ )
+ )
+ if $unit_test->expected_output
+ and $unit_test->expected_output ne '';
+
+ # add the valid regex if defined
+ $model->addStmt(
+ new RDF::Core::Statement(
+ $bnode,
+ $resource->new( MOBY::RDF::Predicates::FETA->validREGEX ),
+ new RDF::Core::Literal( $unit_test->regex )
+ )
+ )
+ if $unit_test->regex
+ and $unit_test->regex ne '';
+
+ # add the valid xpath expression if defined
+ $model->addStmt(
+ new RDF::Core::Statement(
+ $bnode,
+ $resource->new( MOBY::RDF::Predicates::FETA->validXPath ),
+ new RDF::Core::Literal( $unit_test->xpath )
+ )
+ )
+ if $unit_test->xpath
+ and $unit_test->xpath ne '';
+
+ $model->addStmt(
+ new RDF::Core::Statement(
+ $operation,
+ $resource->new( MOBY::RDF::Predicates::FETA->hasUnitTest ),
+ $bnode
+ )
+ );
+ }
+
my $inputs = $SI->input;
foreach (@$inputs) {
- my $inputParameter = new RDF::Core::Resource(
- $self->{instance_uri},
- md5_hex(
- "$service_authority/$service_name/"
- . ($_->isSimple ? "isSimple/" : "isCollection/")
- . MOBY::RDF::Predicates::FETA->inputParameter
- . "/"
- . $_->articleName)
- ); # $node_factory->newResource;
+ my $inputParameter =
+ new RDF::Core::Resource(
+ $self->{instance_uri},
+ md5_hex(
+ "$service_authority/$service_name/"
+ . (
+ $_->isSimple ? "isSimple/" : "isCollection/"
+ )
+ . MOBY::RDF::Predicates::FETA->inputParameter
+ . "/"
+ . $_->articleName
+ )
+ ); # $node_factory->newResource;
$model->addStmt(
new RDF::Core::Statement(
$operation,
@@ -509,18 +617,17 @@
)
);
- my $oType = new RDF::Core::Resource(
- $self->{instance_uri},
- md5_hex(
- "$service_authority/$service_name/"
- . ($_->isSimple ? "isSimple/" : "isCollection/" )
- . MOBY::RDF::Predicates::FETA->inputParameter
- . "/"
- . $_->articleName
- . "/"
- . $_->objectType
- )
- ); # $node_factory->newResource;
+ my $oType =
+ new RDF::Core::Resource(
+ $self->{instance_uri},
+ md5_hex(
+ "$service_authority/$service_name/"
+ . ( $_->isSimple ? "isSimple/" : "isCollection/" )
+ . MOBY::RDF::Predicates::FETA->inputParameter . "/"
+ . $_->articleName . "/"
+ . $_->objectType
+ )
+ ); # $node_factory->newResource;
$model->addStmt(
new RDF::Core::Statement(
$inputParameter,
@@ -535,22 +642,21 @@
$oType,
$resource->new( MOBY::RDF::Predicates::RDF->type ),
new RDF::Core::Resource(
- $self->{datatype_uri}
- . $_->objectType
+ $self->{datatype_uri} . $_->objectType
) #TODO check for lsid
)
);
- my $pType = new RDF::Core::Resource(
- $self->{instance_uri},
- md5_hex(
- "$service_authority/$service_name/"
- . ($_->isSimple ? "isSimple/" : "isCollection/" )
- . MOBY::RDF::Predicates::FETA->hasParameterType
- . "/"
- . $_->articleName
- )
- ); # $node_factory->newResource;
+ my $pType =
+ new RDF::Core::Resource(
+ $self->{instance_uri},
+ md5_hex(
+ "$service_authority/$service_name/"
+ . ( $_->isSimple ? "isSimple/" : "isCollection/" )
+ . MOBY::RDF::Predicates::FETA->hasParameterType . "/"
+ . $_->articleName
+ )
+ ); # $node_factory->newResource;
$model->addStmt(
new RDF::Core::Statement(
$inputParameter,
@@ -571,17 +677,18 @@
);
my $namespaces = $_->namespaces;
foreach my $n (@$namespaces) {
- my $inNamespaces = new RDF::Core::Resource(
- $self->{instance_uri},
+ my $inNamespaces =
+ new RDF::Core::Resource(
+ $self->{instance_uri},
md5_hex(
- "$service_authority/$service_name/"
- . ($_->isSimple ? "isSimple/" : "isCollection/")
- . MOBY::RDF::Predicates::FETA->inputParameter
- . "/"
- . $_->articleName
- . "/"
- . $n)
- ); # $node_factory->newResource;
+ "$service_authority/$service_name/"
+ . ( $_->isSimple ? "isSimple/" : "isCollection/" )
+ . MOBY::RDF::Predicates::FETA->inputParameter
+ . "/"
+ . $_->articleName . "/"
+ . $n
+ )
+ ); # $node_factory->newResource;
$model->addStmt(
new RDF::Core::Statement(
$inputParameter,
@@ -605,13 +712,13 @@
$inNamespaces,
$resource->new( MOBY::RDF::Predicates::RDF->type ),
new RDF::Core::Resource(
- $self->{namespace_uri}
- . $n
+ $self->{namespace_uri} . $n
) #TODO check for lsids
)
);
}
- } elsif ( $_->isCollection ) {
+ }
+ elsif ( $_->isCollection ) {
$model->addStmt(
new RDF::Core::Statement(
@@ -632,16 +739,16 @@
)
);
- my $pType = new RDF::Core::Resource(
- $self->{instance_uri},
- md5_hex(
- "$service_authority/$service_name/"
- . ($_->isSimple ? "isSimple/" : "isCollection/" )
- . MOBY::RDF::Predicates::FETA->hasParameterType
- . "/"
- . $_->articleName
- )
- ); # $node_factory->newResource;
+ my $pType =
+ new RDF::Core::Resource(
+ $self->{instance_uri},
+ md5_hex(
+ "$service_authority/$service_name/"
+ . ( $_->isSimple ? "isSimple/" : "isCollection/" )
+ . MOBY::RDF::Predicates::FETA->hasParameterType . "/"
+ . $_->articleName
+ )
+ ); # $node_factory->newResource;
$model->addStmt(
new RDF::Core::Statement(
$inputParameter,
@@ -663,18 +770,18 @@
my $simples = $_->Simples;
foreach my $simp (@$simples) {
- my $oType = new RDF::Core::Resource(
- $self->{instance_uri},
- md5_hex(
- "$service_authority/$service_name/"
- . ($_->isSimple ? "isSimple/" : "isCollection/" )
- . MOBY::RDF::Predicates::FETA->inputParameter
- . "/"
- . $_->articleName
- . "/"
- . $simp->objectType
- )
- ); # $node_factory->newResource;
+ my $oType =
+ new RDF::Core::Resource(
+ $self->{instance_uri},
+ md5_hex(
+ "$service_authority/$service_name/"
+ . ( $_->isSimple ? "isSimple/" : "isCollection/" )
+ . MOBY::RDF::Predicates::FETA->inputParameter
+ . "/"
+ . $_->articleName . "/"
+ . $simp->objectType
+ )
+ ); # $node_factory->newResource;
$model->addStmt(
new RDF::Core::Statement(
$inputParameter,
@@ -689,24 +796,26 @@
$oType,
$resource->new( MOBY::RDF::Predicates::RDF->type ),
new RDF::Core::Resource(
- $self->{datatype_uri}
- . $simp->objectType
+ $self->{datatype_uri} . $simp->objectType
) #TODO check for lsid
)
);
my $namespaces = $simp->namespaces;
foreach my $n (@$namespaces) {
- my $inNamespaces = new RDF::Core::Resource(
- $self->{instance_uri},
- md5_hex(
- "$service_authority/$service_name/"
- . ($_->isSimple ? "isSimple/" : "isCollection/")
- . MOBY::RDF::Predicates::FETA->inputParameter
- . "/"
- . $_->articleName
- . "/"
- . $n)
- ); # $node_factory->newResource;
+ my $inNamespaces =
+ new RDF::Core::Resource(
+ $self->{instance_uri},
+ md5_hex(
+ "$service_authority/$service_name/"
+ . (
+ $_->isSimple ? "isSimple/" : "isCollection/"
+ )
+ . MOBY::RDF::Predicates::FETA->inputParameter
+ . "/"
+ . $_->articleName . "/"
+ . $n
+ )
+ ); # $node_factory->newResource;
$model->addStmt(
new RDF::Core::Statement(
$inputParameter,
@@ -735,8 +844,7 @@
MOBY::RDF::Predicates::RDF->type
),
new RDF::Core::Resource(
- $self->{namespace_uri}
- . $n
+ $self->{namespace_uri} . $n
) #TODO check for lsids
)
);
@@ -749,15 +857,17 @@
foreach (@$secondaries) {
next unless $_->isSecondary;
- my $inputParameter = new RDF::Core::Resource(
- $self->{instance_uri},
- md5_hex(
- "$service_authority/$service_name/"
- . "isSecondaryInputParameter/"
- . MOBY::RDF::Predicates::FETA->inputParameter
- . "/"
- . $_->articleName)
- ); #$node_factory->newResource;
+ my $inputParameter =
+ new RDF::Core::Resource(
+ $self->{instance_uri},
+ md5_hex(
+ "$service_authority/$service_name/"
+ . "isSecondaryInputParameter/"
+ . MOBY::RDF::Predicates::FETA->inputParameter
+ . "/"
+ . $_->articleName
+ )
+ ); #$node_factory->newResource;
$model->addStmt(
new RDF::Core::Statement(
$operation,
@@ -777,16 +887,17 @@
)
);
- my $pType = new RDF::Core::Resource(
- $self->{instance_uri},
- md5_hex(
- "$service_authority/$service_name/"
- . "isSecondary/"
- . MOBY::RDF::Predicates::FETA->hasParameterType
- . "/"
- . $_->articleName
- )
- ); # $node_factory->newResource;
+ my $pType =
+ new RDF::Core::Resource(
+ $self->{instance_uri},
+ md5_hex(
+ "$service_authority/$service_name/"
+ . "isSecondary/"
+ . MOBY::RDF::Predicates::FETA->hasParameterType
+ . "/"
+ . $_->articleName
+ )
+ ); # $node_factory->newResource;
$model->addStmt(
new RDF::Core::Statement(
$inputParameter,
@@ -822,8 +933,7 @@
$resource->new( MOBY::RDF::Predicates::FETA->min ),
new RDF::Core::Literal( $_->min )
)
- )
- if defined( $_->min );
+ ) if defined( $_->min );
$model->addStmt(
new RDF::Core::Statement(
@@ -831,8 +941,7 @@
$resource->new( MOBY::RDF::Predicates::FETA->max ),
new RDF::Core::Literal( $_->max )
)
- )
- if defined( $_->max );
+ ) if defined( $_->max );
$model->addStmt(
new RDF::Core::Statement(
@@ -852,8 +961,7 @@
),
new RDF::Core::Literal( $_->default )
)
- )
- if defined( $_->default );
+ ) if defined( $_->default );
$model->addStmt(
new RDF::Core::Statement(
@@ -875,15 +983,18 @@
my $outputs = $SI->output;
foreach (@$outputs) {
- my $outputParameter = new RDF::Core::Resource(
- $self->{instance_uri},
- md5_hex(
- "$service_authority/$service_name/"
- . ($_->isSimple ? "isSimple/" : "isCollection/")
- . MOBY::RDF::Predicates::FETA->outputParameter
- . "/"
- . $_->articleName)
- ); # $node_factory->newResource;
+ my $outputParameter =
+ new RDF::Core::Resource(
+ $self->{instance_uri},
+ md5_hex(
+ "$service_authority/$service_name/"
+ . (
+ $_->isSimple ? "isSimple/" : "isCollection/" )
+ . MOBY::RDF::Predicates::FETA->outputParameter
+ . "/"
+ . $_->articleName
+ )
+ ); # $node_factory->newResource;
$model->addStmt(
new RDF::Core::Statement(
$operation,
@@ -913,18 +1024,17 @@
)
);
- my $oType = new RDF::Core::Resource(
- $self->{instance_uri},
- md5_hex(
- "$service_authority/$service_name/"
- . ($_->isSimple ? "isSimple/" : "isCollection/" )
- . MOBY::RDF::Predicates::FETA->outputParameter
- . "/"
- . $_->articleName
- . "/"
- . $_->objectType
- )
- ); # $node_factory->newResource;
+ my $oType =
+ new RDF::Core::Resource(
+ $self->{instance_uri},
+ md5_hex(
+ "$service_authority/$service_name/"
+ . ( $_->isSimple ? "isSimple/" : "isCollection/" )
+ . MOBY::RDF::Predicates::FETA->outputParameter . "/"
+ . $_->articleName . "/"
+ . $_->objectType
+ )
+ ); # $node_factory->newResource;
$model->addStmt(
new RDF::Core::Statement(
$outputParameter,
@@ -939,22 +1049,21 @@
$oType,
$resource->new( MOBY::RDF::Predicates::RDF->type ),
new RDF::Core::Resource(
- $self->{datatype_uri}
- . $_->objectType
+ $self->{datatype_uri} . $_->objectType
) #TODO check for lsid
)
);
- my $pType = new RDF::Core::Resource(
- $self->{instance_uri},
- md5_hex(
- "$service_authority/$service_name/"
- . ($_->isSimple ? "isSimple/" : "isCollection/" )
- . MOBY::RDF::Predicates::FETA->hasParameterType
- . "/"
- . $_->articleName
- )
- ); # $node_factory->newResource;
+ my $pType =
+ new RDF::Core::Resource(
+ $self->{instance_uri},
+ md5_hex(
+ "$service_authority/$service_name/"
+ . ( $_->isSimple ? "isSimple/" : "isCollection/" )
+ . MOBY::RDF::Predicates::FETA->hasParameterType . "/"
+ . $_->articleName
+ )
+ ); # $node_factory->newResource;
$model->addStmt(
new RDF::Core::Statement(
$outputParameter,
@@ -975,17 +1084,18 @@
);
my $namespaces = $_->namespaces;
foreach my $n (@$namespaces) {
- my $inNamespaces = new RDF::Core::Resource(
- $self->{instance_uri},
+ my $inNamespaces =
+ new RDF::Core::Resource(
+ $self->{instance_uri},
md5_hex(
- "$service_authority/$service_name/"
- . ($_->isSimple ? "isSimple/" : "isCollection/")
- . MOBY::RDF::Predicates::FETA->outputParameter
- . "/"
- . $_->articleName
- . "/"
- . $n)
- ); # $node_factory->newResource;
+ "$service_authority/$service_name/"
+ . ( $_->isSimple ? "isSimple/" : "isCollection/" )
+ . MOBY::RDF::Predicates::FETA->outputParameter
+ . "/"
+ . $_->articleName . "/"
+ . $n
+ )
+ ); # $node_factory->newResource;
$model->addStmt(
new RDF::Core::Statement(
$outputParameter,
@@ -1009,13 +1119,13 @@
$inNamespaces,
$resource->new( MOBY::RDF::Predicates::RDF->type ),
new RDF::Core::Resource(
- $self->{namespace_uri}
- . $n
+ $self->{namespace_uri} . $n
) #TODO check for lsids
)
);
}
- } elsif ( $_->isCollection ) {
+ }
+ elsif ( $_->isCollection ) {
$model->addStmt(
new RDF::Core::Statement(
@@ -1036,16 +1146,16 @@
)
);
- my $pType = new RDF::Core::Resource(
- $self->{instance_uri},
- md5_hex(
- "$service_authority/$service_name/"
- . ($_->isSimple ? "isSimple/" : "isCollection/" )
- . MOBY::RDF::Predicates::FETA->hasParameterType
- . "/"
- . $_->articleName
- )
- ); # $node_factory->newResource;
+ my $pType =
+ new RDF::Core::Resource(
+ $self->{instance_uri},
+ md5_hex(
+ "$service_authority/$service_name/"
+ . ( $_->isSimple ? "isSimple/" : "isCollection/" )
+ . MOBY::RDF::Predicates::FETA->hasParameterType . "/"
+ . $_->articleName
+ )
+ ); # $node_factory->newResource;
$model->addStmt(
new RDF::Core::Statement(
$outputParameter,
@@ -1067,18 +1177,18 @@
my $simples = $_->Simples;
foreach my $simp (@$simples) {
- my $oType = new RDF::Core::Resource(
- $self->{instance_uri},
- md5_hex(
- "$service_authority/$service_name/"
- . ($_->isSimple ? "isSimple/" : "isCollection/" )
- . MOBY::RDF::Predicates::FETA->outputParameter
- . "/"
- . $_->articleName
- . "/"
- . $simp->objectType
- )
- ); # $node_factory->newResource;
+ my $oType =
+ new RDF::Core::Resource(
+ $self->{instance_uri},
+ md5_hex(
+ "$service_authority/$service_name/"
+ . ( $_->isSimple ? "isSimple/" : "isCollection/" )
+ . MOBY::RDF::Predicates::FETA->outputParameter
+ . "/"
+ . $_->articleName . "/"
+ . $simp->objectType
+ )
+ ); # $node_factory->newResource;
$model->addStmt(
new RDF::Core::Statement(
$outputParameter,
@@ -1093,24 +1203,26 @@
$oType,
$resource->new( MOBY::RDF::Predicates::RDF->type ),
new RDF::Core::Resource(
- $self->{datatype_uri}
- . $simp->objectType
+ $self->{datatype_uri} . $simp->objectType
) #TODO check for lsid
)
);
my $namespaces = $simp->namespaces;
foreach my $n (@$namespaces) {
- my $inNamespaces = new RDF::Core::Resource(
- $self->{instance_uri},
- md5_hex(
- "$service_authority/$service_name/"
- . ($_->isSimple ? "isSimple/" : "isCollection/")
- . MOBY::RDF::Predicates::FETA->outputParameter
- . "/"
- . $_->articleName
- . "/"
- . $n)
- ); # $node_factory->newResource;
+ my $inNamespaces =
+ new RDF::Core::Resource(
+ $self->{instance_uri},
+ md5_hex(
+ "$service_authority/$service_name/"
+ . (
+ $_->isSimple ? "isSimple/" : "isCollection/"
+ )
+ . MOBY::RDF::Predicates::FETA->outputParameter
+ . "/"
+ . $_->articleName . "/"
+ . $n
+ )
+ ); # $node_factory->newResource;
$model->addStmt(
new RDF::Core::Statement(
$outputParameter,
@@ -1139,8 +1251,7 @@
MOBY::RDF::Predicates::RDF->type
),
new RDF::Core::Resource(
- $self->{namespace_uri}
- . $n
+ $self->{namespace_uri} . $n
) #TODO check for lsids
)
);
@@ -1150,11 +1261,12 @@
}
}
my $xml = '';
- my $serializer = new RDF::Core::Model::Serializer(
- Model => $model,
- Output => \$xml,
- BaseURI => 'URI://BASE/',
- );
+ my $serializer =
+ new RDF::Core::Model::Serializer(
+ Model => $model,
+ Output => \$xml,
+ BaseURI => 'URI://BASE/',
+ );
$serializer->serialize;
return $xml;
}
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