[MOBY-guts] biomoby commit
Frank Gibbons
fgibbons at pub.open-bio.org
Fri Sep 16 17:01:11 UTC 2005
fgibbons
Fri Sep 16 13:01:11 EDT 2005
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv23895/MOBY/Client
Modified Files:
Central.pm
Log Message:
- Clean up some regular expressions, make easier to read.
- ref operator returns scalar (string), so we should use string comparison.
- Remove redundant "Title" in docs. That's what =head2 is for.
- Clean up setting default values using short-circuiting || operator.
moby-live/Perl/MOBY/Client Central.pm,1.123,1.124
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v
retrieving revision 1.123
retrieving revision 1.124
diff -u -r1.123 -r1.124
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2005/08/31 22:32:27 1.123
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2005/09/16 17:01:10 1.124
@@ -55,6 +55,9 @@
be sufficient for most or all MOBY Client activities written in Perl.
+=cut
+
+
=head1 AUTHORS
Mark Wilkinson (markw at illuminae.com)
@@ -70,7 +73,6 @@
=head2 new
- Title : new
Usage : my $MOBY = MOBY::Client::Central->new(Registries => \%regrefs)
Function : connect to one or more MOBY-Central
registries for searching
@@ -140,8 +142,7 @@
(
Connections => [ undef, 'read/write' ],
default_MOBY_servername => [ 'mobycentral', 'read/write' ],
- default_MOBY_server => [
-
+ default_MOBY_server => [
'http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl',
'read/write'
],
@@ -239,119 +240,119 @@
}
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;
-
- # 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 ) {
- $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' => $proxy ] );
- }
- else {
- @soapargs = ($url);
- }
- push @{ $self->Connections }, [
- $name, $type,
- SOAP::Lite->proxy(@soapargs)->uri($uri)->on_fault(
- sub {
- my ( $soap, $res ) = @_;
- die ref $res
- ? $res->faultstring
- : $soap->transport->status,
- "\n ERROR ERROR ERROR\n";
- }
- )
- ];
- }
- }
- $self->multiple_registries( $regno - 1 )
- ; # one is not "multiple", it is just a change in default -> set to "false" if only one
+ 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;
+
+ # 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 ) {
+ $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 ] );
}
else {
- $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)->uri( $self->default_MOBY_uri )
- ->on_fault(
- sub {
- my ( $soap, $res ) = @_;
- die ref $res
- ? $res->faultstring
- : $soap->transport->status, "\n ERROR ERROR ERROR\n";
- }
- )
- ];
- }
+ @soapargs = ($url);
}
- return undef unless $self->Connection(); # gotta have at least one...
- return $self;
+ push @{ $self->Connections },
+ [
+ $name, $type,
+ SOAP::Lite->proxy(@soapargs)->uri($uri)->on_fault(
+ sub {
+ my ( $soap, $res ) = @_;
+ die ref $res
+ ? $res->faultstring
+ : $soap->transport->status,
+ "\n ERROR ERROR ERROR\n";
+ }
+ )
+ ];
+ }
+ }
+ $self->multiple_registries( $regno - 1 )
+ ; # one is not "multiple", it is just a change in default -> set to "false" if only one
+ }
+ else {
+ $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)->uri( $self->default_MOBY_uri )
+ ->on_fault(
+ sub {
+ my ( $soap, $res ) = @_;
+ die ref $res
+ ? $res->faultstring
+ : $soap->transport->status, "\n ERROR ERROR ERROR\n";
+ }
+ )
+ ];
+ }
+ }
+ return undef unless $self->Connection(); # gotta have at least one...
+ return $self;
}
=head2 registerObject a.k.a registerObjectClass
- Title : registerObject ; registerObjectClass
Usage : $REG = $MOBY->registerObject(%args)
Usage : $REG = $MOBY->registerObjectClass(%args)
Function : register a new type of MOBY Object
@@ -383,18 +384,13 @@
"Contact email address (contactEmail parameter) is required for object registration"
)
if ( !$a{contactEmail} );
- my $term = $a{'objectType'};
- $term ||= "";
- my $desc = $a{'description'};
- $desc ||= "";
+ my $term = $a{'objectType'} || "";
+ my $desc = $a{'description'} || "";
if ( $desc =~ /<!\[CDATA\[((?>[^\]]+))\]\]>/ ) {
$desc = $1;
}
- my $contactEmail = $a{'contactEmail'};
- $contactEmail ||= "";
- my $authURI = $a{'authURI'};
- $authURI ||= "";
- $authURI ||= "";
+ my $contactEmail = $a{'contactEmail'} || "";
+ my $authURI = $a{'authURI'} || "";
my %Relationships = %{ $a{'Relationships'} };
my $clobber = $a{'Clobber'} ? $a{'Clobber'} : 0;
my $message = "<registerObjectClass>
@@ -427,7 +423,6 @@
=head2 deregisterObject a.k.a. deregisterObjectClass
- Title : deregisterObject ; deregisterObjectClass
Usage : $REG = $MOBY->deregisterObject(%args)
Usage : $REG = $MOBY->deregisterObjectClass(%args)
Function : deregister a MOBY Object
@@ -447,8 +442,7 @@
return $self->errorRegXML(
"Function not allowed when querying multiple registries")
if $self->multiple_registries;
- my $id = $a{'objectType'};
- $id ||= "";
+ my $id = $a{'objectType'} || "";
my $message = "
<deregisterObjectClass>
<objectType>$id</objectType>
@@ -461,7 +455,6 @@
=head2 retrieveObjectDefinition
- Title : retrieveObjectDefinition
Usage : $DEF = $MOBY->retrieveObjectDefinition($objectType[,$registry])
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
@@ -567,7 +560,6 @@
=head2 registerServiceType
- Title : registerServiceType
Usage : $REG = $MOBY->registerServiceType(%args)
Function : register a new MOBY Service type
Returns : MOBY::Registration object
@@ -585,17 +577,14 @@
return $self->errorRegXML(
"Function not allowed when querying multiple registries")
if $self->multiple_registries;
- my $type = $a{'serviceType'};
- $type ||= "";
+ my $type = $a{'serviceType'} || "";
my $desc = $a{'description'};
if ( $desc =~ /<!\[CDATA\[((?>[^\]]+))\]\]>/ ) {
$desc = $1;
}
$desc ||= "";
- my $email = $a{'contactEmail'};
- $email ||= "";
- my $auth = $a{'authURI'};
- $auth ||= "";
+ my $email = $a{'contactEmail'} || "";
+ my $auth = $a{'authURI'} || "";
my %Relationships = %{ $a{'Relationships'} };
my $message = "
<registerServiceType>
@@ -620,7 +609,6 @@
=head2 deregisterServiceType
- Title : deregisterServiceType
Usage : $REG = $MOBY->deregisterServiceType(%args)
Function : deregister a deprecated MOBY Service Type
Returns : MOBY::Registration object
@@ -634,8 +622,7 @@
return $self->errorRegXML(
"Function not allowed when querying multiple registries")
if $self->multiple_registries;
- my $id = $a{'serviceType'};
- $id ||= "";
+ my $id = $a{'serviceType'} || "";
my $message = "
<deregisterServiceType>
<serviceType>$id</serviceType>
@@ -648,7 +635,6 @@
=head2 registerNamespace
- Title : registerNamespace
Usage : $REG = $MOBY->registerNamespace(%args)
Function : register a new Namespace
Returns : MOBY::Registration object
@@ -665,17 +651,14 @@
return $self->errorRegXML(
"Function not allowed when querying multiple registries")
if $self->multiple_registries;
- my $type = $a{'namespaceType'};
- $type ||= "";
- my $authURI = $a{'authURI'};
- $authURI ||= "";
+ my $type = $a{'namespaceType'} || "";
+ my $authURI = $a{'authURI'} || "";
my $desc = $a{'description'};
if ( $desc =~ /<!\[CDATA\[((?>[^\]]+))\]\]>/ ) {
$desc = $1;
}
$desc ||= "";
- my $contact = $a{'contactEmail'};
- $contact ||= "";
+ my $contact = $a{'contactEmail'} || "";
my $message = "
<registerNamespace>
<namespaceType>$type</namespaceType>
@@ -691,7 +674,6 @@
=head2 deregisterNamespace
- Title : deregisterNamespace
Usage : $REG = $MOBY->deregisterNamespace(%args)
Function : deregister a deprecated MOBY Namespace
Returns : MOBY::Registration object
@@ -705,8 +687,7 @@
return $self->errorRegXML(
"Function not allowed when querying multiple registries")
if $self->multiple_registries;
- my $id = $a{'namespaceType'};
- $id ||= "";
+ my $id = $a{'namespaceType'} || "";
my $message = "
<deregisterNamespace>
<namespaceType>$id</namespaceType>
@@ -719,7 +700,6 @@
=head2 registerService
- Title : registerService
Usage : $REG = $MOBY->registerService(%args)
Function : register a new MOBY Service instance
Returns : MOBY::Registration object
@@ -774,24 +754,17 @@
return $self->errorRegXML(
"Function not allowed when querying multiple registries")
if $self->multiple_registries;
- my $name = $a{serviceName};
- $name ||= "";
- my $type = $a{serviceType};
- $type ||= "";
- my $authURI = $a{authURI};
- $authURI ||= "";
- my $email = $a{contactEmail};
- $email ||= "";
- my $URL = $a{URL};
- $URL ||= "";
- my $desc = $a{description};
- $desc ||= "";
+ 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;
}
- my $signatureURL = $a{signatureURL};
- $signatureURL ||= "";
+ my $signatureURL = $a{signatureURL} || "";
my $Category = lc( $a{category} );
chomp $Category;
$Category ||= "";
@@ -856,10 +829,10 @@
if ( $Category eq "moby" || $Category eq 'soap' ) {
my %SEC;
- if ( $a{'secondary'} && ( ref( $a{'secondary'} ) =~ /hash/i ) ) {
+ if ( $a{'secondary'} && ( ref( $a{'secondary'} ) eq 'HASH' ) ) {
%SEC = %{ $a{secondary} };
}
- elsif ( $a{'secondary'} && !( ref( $a{'secondary'} ) =~ /hash/i ) ) {
+ elsif ( $a{'secondary'} && ( ref( $a{'secondary'} ) ne 'HASH' ) ) {
return $self->errorRegXML(
"invalid structure of secondary parameters. Expected hashref."
);
@@ -880,11 +853,11 @@
my ( $articleName, $def ) = @{$article};
$articleName ||= "";
my @Objects; #
- unless ( (ref($def) =~ /array/i)) { # $def = [objType => \@ns] or $def=[[objType => \@ns]]
+ unless ( ref($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] ) =~ /array/i ) { # collection $def->[0] = [objType => \@ns]
+ if ( ( ref $def->[0] ) eq 'ARRAY' ) { # collection $def->[0] = [objType => \@ns]
# def= [[objType2 => [ns3, ns4...]], ...]
$message .= "<Collection articleName='$articleName'>\n";
if (scalar(@{$def->[0]} > 2)){
@@ -899,7 +872,7 @@
@objectdefs = ($def);
}
foreach my $objectdef (@objectdefs) {
- if ( ( ref( $def->[0] ) ) =~ /array/i ) {
+ if ( ref( $def->[0] ) eq 'ARRAY' ) {
$message .= "<Simple>\n";
}
else {
@@ -908,7 +881,7 @@
my ( $type, $Namespaces ) = @{$objectdef};
$type ||= "";
$message .= "<objectType>$type</objectType>\n";
- unless ( ref($Namespaces) =~ /array/i ) {
+ unless ( ref($Namespaces) eq 'ARRAY' ) {
return $self->errorRegXML(
"invalid structure of $inout namespaces for object $type in article $articleName; expected arrayref"
);
@@ -918,7 +891,7 @@
}
$message .= "</Simple>\n";
}
- if ( ( ref( $def->[0] ) ) =~ /array/i ) {
+ if ( ref( $def->[0] ) eq 'ARRAY' ) {
$message .= "</Collection>\n";
}
}
@@ -939,7 +912,7 @@
#
$message .= "<secondaryArticles>\n";
while ( my ( $param, $desc ) = each %SEC ) {
- unless ( ( ref($desc) ) =~ /hash/i ) {
+ unless ( ref($desc) eq 'HASH' ) {
return $self->errorRegXML( "invalid structure of secondary article $param; expected hashref of limitations"
);
}
@@ -953,15 +926,12 @@
return $self->errorRegXML("a secondaryArticle must contain at least a datatype value in secondary article $param"
);
}
- unless ( ( $datatype =~ /Integer/ )
- || ( $datatype =~ /Float/ )
- || ( $datatype =~ /String/ )
- || ( $datatype =~ /DateTime/ ) )
+ unless ( $datatype =~ /Integer|Float|String|DateTime/ )
{
return $self->errorRegXML("a secondaryArticle must have a datatype of Integer, Float, String, or DateTime"
);
}
- unless ( ( ref($enums) ) =~ /array/i ) {
+ unless ( ref($enums) eq 'ARRAY' ) {
return $self->errorRegXML("invalid structure of enum limits in secondary article $param; expected arrayref"
);
}
@@ -1029,9 +999,7 @@
=head2 registerServiceWSDL
- Title : registerServiceWSDL
- Usage : not yet implemented
-
+ Usage : Needs documentation
=cut
@@ -1050,7 +1018,6 @@
=head2 deregisterService
- Title : deregisterService
Usage : $REG = $MOBY->deregisterService(%args)
Function : deregister a registered MOBY Service
Returns : MOBY::Registration object
@@ -1087,7 +1054,6 @@
=head2 findService
- Title : findService
Usage : ($ServiceInstances, $RegObject) = $MOBY->findService(%args)
Function : Find services that match certain search criterion
Returns : ON SUCCESS: arrayref of MOBY::Client::ServiceInstance objects, and undef
@@ -1123,23 +1089,15 @@
my ( $self, %a ) = @_;
my $reg = ( $a{Registry} ) ? $a{Registry} : $self->default_MOBY_servername;
my $id = $a{'serviceID'};
- my $servicename = $a{'serviceName'};
- $servicename ||= "";
- my $authoritative = $a{'authoritative'};
- $authoritative ||= 0;
- my $serviceType = $a{'serviceType'};
- $serviceType ||= "";
- my $authURI = $a{'authURI'};
- $authURI ||= "";
- my $category = $a{'category'};
- $category ||= "moby";
- my $exObj = $a{'expandObjects'};
- $exObj ||= 0;
- my $exServ = $a{'expandServices'};
- $exServ ||= 0;
- my $kw = $a{'keywords'};
- $kw ||= [];
- ref($kw) =~ /array/i || return (
+ my $servicename = $a{'serviceName'} || "";
+ my $authoritative = $a{'authoritative'} || 0;
+ my $serviceType = $a{'serviceType'} || "";
+ my $authURI = $a{'authURI'} || "";
+ my $category = $a{'category'} || "moby";
+ my $exObj = $a{'expandObjects'} || 0;
+ my $exServ = $a{'expandServices'} || 0;
+ my $kw = $a{'keywords'} || [];
+ ref($kw) eq 'ARRAY' || return (
undef,
$self->errorRegXML(
"invalid structure of keywords. Expected arrayref"
@@ -1168,7 +1126,7 @@
#$a{input} = [[]] unless (defined $a{input});
#$a{output} = [[]] unless (defined $a{output});
- if ( defined $a{input} && !( ref( $a{input} ) =~ /array/i ) ) {
+ if ( defined $a{input} && ( ref( $a{input} ) ne 'ARRAY' ) ) {
return (
undef,
$self->errorRegXML(
@@ -1176,7 +1134,7 @@
)
);
}
- if ( defined $a{output} && !( ref( $a{output} ) =~ /array/i ) ) {
+ if ( defined $a{output} && ( ref( $a{output} ) ne 'ARRAY' ) ) {
return (
undef,
$self->errorRegXML(
@@ -1198,12 +1156,12 @@
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) =~ /ARRAY/ );
+ 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) =~ /array/i ) {
+ unless ( ref($param) eq 'ARRAY' ) {
return (
undef,
$self->errorRegXML(
@@ -1216,7 +1174,7 @@
#warn "no namespace part of the param" unless defined $namespaces;
my @objectdefs;
- if ( ( ref $class ) =~ /array/i ) { # collection
+ if ( ref $class eq 'ARRAY' ) { # collection
$message .= "<Collection>\n";
@objectdefs = $class;
}
@@ -1229,7 +1187,7 @@
die "type is missing from objectdef " unless $type;
$message .= "<objectType>$type</objectType>\n";
if ( defined($Namespaces)
- && !( ref($Namespaces) =~ /array/i ) )
+ && ( ref($Namespaces) ne 'ARRAY' ) )
{
return (
undef,
@@ -1244,7 +1202,7 @@
}
$message .= "</Simple>\n";
}
- if ( ( ref($class) ) =~ /array/i ) {
+ if ( ref($class) eq 'ARRAY' ) {
$message .= "</Collection>\n";
}
}
@@ -1259,7 +1217,6 @@
=head2 retrieveService
- Title : retrieveService
Usage : $WSDL = $MOBY->retrieveService($ServiceInstance)
Function : get the WSDL definition of the service with this name/authority URI
Returns : a WSDL string
@@ -1304,7 +1261,6 @@
=head2 retrieveResourceURLs
- Title : 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
@@ -1336,7 +1292,6 @@
=head2 retrieveServiceNames
- Title : retrieveServiceNames(%args)
Usage : $names = $MOBY->retrieveServiceNames([$reg_name])
Function : get a (redundant) list of all registered service names
(N.B. NOT service types!)
@@ -1382,7 +1337,6 @@
=head2 retrieveServiceProviders
- Title : retrieveServiceProviders
Usage : @URIs = $MOBY->retrieveServiceProviders([$reg_name])
Function : get the list of all provider's AuthURI's
Returns : list of service provider URI strings
@@ -1413,7 +1367,6 @@
=head2 retrieveServiceTypes
- Title : retrieveServiceTypes(%args)
Usage : $types = $MOBY->retrieveServiceTypes([$reg_name])
Function : get the list of all registered service types
Returns : hashref of $types{$type} = $definition
@@ -1463,7 +1416,6 @@
=head2 retrieveObjectNames
- Title : retrieveObjectNames(%args)
Usage : $names = $MOBY->retrieveObjectNames([$reg_name])
Function : get the list of all registered Object types
Returns : hashref of hash:
@@ -1511,7 +1463,6 @@
=head2 retrieveNamespaces
- Title : retrieveNamespaces(%args)
Usage : $ns = $MOBY->retrieveNamespaces([$reg_name])
Function : get the list of all registered Namespace types
Returns : hashref of hash:
@@ -1562,7 +1513,6 @@
=head2 retrieveObject
- Title : retrieveObject
Usage : $objects = $MOBY->retrieveObjectNames(%args)
Function : get the object xsd
Returns : hashref of hash:
@@ -1616,7 +1566,6 @@
=head2 Relationships
- Title : Relationships
Usage : $def = $MOBY->Relationships(%args)
Function : traverse and return the relationships in the ontology
Returns : hashref of $hash{relationship_type}=\@lsids
@@ -1639,7 +1588,7 @@
my @relationships;
@relationships = @{ $args{'Relationships'} }
if ( $args{'Relationships'}
- && ( ref( $args{'Relationships'} ) =~ /array/i ) );
+ && ( ref( $args{'Relationships'} ) eq 'ARRAY' ) );
push @relationships, 'isa' unless $relationships[0]; # need to have at least one relationship
my $reg = $args{'Registry'};
my $m;
@@ -1714,7 +1663,6 @@
=head2 ISA
- Title : ISA
Usage : $def = $MOBY->ISA($class1, $class2)
Function : a pre-canned use of the Relationships function
to quickly get an answer to whether class1 ISA class2
@@ -1760,8 +1708,6 @@
=head2 DUMP
-
- Title : DUMP
Usage : ($mobycentral, $mobyobject, $mobyservice, $mobynamespace, $mobyrelationship) = $MOBY->DUMP(['registry'])
Function : DUMP the mysql for the current MOBY Central database
Returns : text
@@ -1919,7 +1865,6 @@
=head2 LSID_CACHE
- Title : LSID_CACHE
Usage : $lsid = $MOBY->LSID_CACHE($term, $lsid)
Function : get/set LSID from the cache
Returns : lsid as a scalar
@@ -1944,7 +1889,6 @@
=head2 ISA_CACHE
- Title : 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
@@ -1959,7 +1903,7 @@
sub ISA_CACHE {
my ( $self, $desiredterm, $isas ) = @_;
my $term = $desiredterm;
- return (undef) if $isas && !( ref($isas) =~ /ARRAY/ );
+ return (undef) if $isas && ( ref($isas) ne 'ARRAY');
if ( $term && $isas ) {
my @isalsids;
foreach (@$isas){
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