MOBY::Client::Central |
MOBY::Client::Central - a client side wrapper for MOBY Central
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";
}
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.
Mark Wilkinson (markw@illuminae.com)
BioMOBY Project: http://www.biomoby.org
Title : new Usage : my $MOBY = MOBY::Client::Central->new(Registries => \%regrefs) Function : connect to one or more MOBY-Central registries for searching Returns : MOBY::Client::Central object
ENV & PROXY : you can set environment variables to change the defaults. By default, a call to 'new' will initialize MOBY::Client::Central to connect to the MOBY Central registry at: http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral.pl If you wish to chose another registry by default, or if you need to set up additional connection details (e.g. PROXY) then you may set the following environment variables to whatever you require: MOBY_SERVER (default http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral.pl) MOBY_URI (default http://mobycentral.cbr.nrc.ca/MOBY/Central) MOBY_PROXY (no default)
Args : Registries - optional. - takes the form {$NAME1 => { URL => $URL, URI => $URI, PROXY => $proxy_server}, $NAME2 => { URL => $URL, URI => $URI, PROXY => $proxy_server}, } - by default this becomes {mobycentral => { URL => 'http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral.pl', URI => 'http://mobycentral.cbr.nrc.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
Title : registerObject ; 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 => [ [Object1, articleName], [Object2, articleName]], relationshipType2 => [ [Object1, articleName]]}
Title : deregisterObject ; 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)
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 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" description => "a human-readable description of the object" contactEmail => "your@email.address" authURI => "URI of the registrar of this object" Relationships => { relationshipType1 => [ [Object1, articleName], [Object2, articleName]], relationshipType2 => [ [Object1, articleName]]} XML => <....XML of object registration.../>
Args : objectType => the name or LSID URI for an object
Title : 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"
Title : deregisterServiceType Usage : $REG = $MOBY->deregisterServiceType(%args) Function : deregister a deprecated MOBY Service Type Returns : MOBY::Registration object Args : serviceType => $serviceType (from ontology)
Title : 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)
Title : deregisterNamespace Usage : $REG = $MOBY->deregisterNamespace(%args) Function : deregister a deprecated MOBY Namespace Returns : MOBY::Registration object Args : namespaceType => $mynamespaceType (from ontology)
Title : 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" | "wsdl" (currently only moby and wsdl supported) 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, default => DEFAULT, max => MAX, min => MIN, enum => [one, two]}, parametername2 => { datatype => TYPE, default => DEFAULT, max => MAX, min => MIN, enum => [one, two]} }
Title : registerServiceWSDL Usage : not yet implemented
Title : deregisterService Usage : $REG = $MOBY->deregisterService(%args) Function : deregister a registered MOBY Service Returns : MOBY::Registration object Args : serviceID => $serviceID
Title : findService Usage : ($ServiceInstances, $RegObject) = $MOBY->findService(%args) Function : Find services that match certain search criterion Returns : ON SUCCESS: arrayref of MOBY::Client::ServiceInstance objects, and undef 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" | "soap" (currently only moby supported) (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 ]
Title : 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)
Title : retrieveServiceNames Usage : $names = $MOBY->retrieveServiceNames([$reg_name]) 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 : $reg_name: name of registry you wish to retrieve from (optional)
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 Args : $reg_name: name of registry you wish to retrieve from (optional)
Title : retrieveServiceTypes Usage : $types = $MOBY->retrieveServiceTypes([$reg_name]) Function : get the list of all registered service types Returns : hashref of $types{$type} = $definition Args : $reg_name: name of registry you wish to retrieve from (optional)
Title : retrieveObjectNames Usage : $names = $MOBY->retrieveObjectNames([$reg_name]) Function : get the list of all registered Object types Returns : hashref of hash: $names{$name} = $definition Args : $reg_name: name of registry you wish to retrieve from (optional)
Title : retrieveNamespaces Usage : $ns = $MOBY->retrieveNamespaces([$reg_name]) Function : get the list of all registered Namespace types Returns : hashref of hash: $ns{$namespace} = $definition Args : $reg_name: name of registry you wish to retrieve from (optional)
NOT YET IMPLEMENTED Title : retrieveObject Usage : $objects = $MOBY->retrieveObjectNames($reg, $name | "all") Function : get the object xsd Returns : hashref of hash: $objects{$name} = $W3C_XML_Schema_string Args : $reg - name of MOBY Central you want to use (must pass undef otherwise) $name - object name (from ontology) or "all" to get all objects
Title : Relationships Usage : $def = $MOBY->Relationships(%args) Function : traverse and return the relationships in the ontology Returns : hashref of $hash{relationship_type}=\@lsids 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)
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 Returns : Boolean Args : $class1 - an Object ontology term or LSID $class2 - an Object ontology term or LSID
Title : DUMP Usage : ($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
Title : 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.
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 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!!!
MOBY::Client::Central |