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public interface Central
An interface that outlines the methods needed to query a Moby central
registry. To fully implement a Mobycentral registry, Registry
must also be implemented.
| Method Summary | |
|---|---|
String |
findService(String serviceQueryObject)
Locate a service instance, matching various characteristics, such as the provider name, the kind of input expected by the service, the kind of output it provides, etc. |
String |
Relationships(String query)
Retrieve a list of MOBY object classes having a specified relationship with the given class |
String |
retrieveNamespaces()
Retrieve a list of all registered namespaces |
String |
retrieveObjectDefinitions(String query)
Retrieve the class definition, in the form of the full registration details for the class type specified by the input XML. |
String |
retrieveObjectNames()
Retrieve the definitions and registration details of all registered object types. |
String |
retrieveObjectSchema(String query)
Retrieve an XML schema representation of a particular object class. |
String |
retrieveResourceURLs()
Retrieve the URLs of all registered services. |
String |
retrieveService(String query)
Retrieve the definition for a service instance, as specified in WSDL format. |
String |
retrieveServiceNames()
Retrieve the names of all registered services. |
String |
retrieveServiceProviders()
Retrieve the names of all registered service providers. |
String |
retrieveServiceTypes()
Retrieve the definitions and registration details of all registered service types. |
| Method Detail |
|---|
String findService(String serviceQueryObject)
serviceQueryObject - a service query object like the following:
<findService>
<!-- Service Query Object -->
</findService>
where a Service Query Object contains a Query Object that allows a user
to query Moby Central.
To query MOBY Central, you fill out the relevant elements of a Query
Object. These include the input and/or output data Classes (by name
from the Class ontology), the Service-type (by name from the Service-type
ontology), the authority (service provider URI), or any number of
keywords that must appear in the service description.
* MOBY Central finds all services which match the contents of
the Query Object.
* All elements are optional, however at least one must be
present.
* All elements present are considered to be increasingly
limiting on the search (i.e. "AND").
* keywords are:
o one keyword or fragment per keyword element
o wildcard "*" is allowed in combination with
keyword fragments and or sentence fragments
(lone "*" is meaningless and ignored)
o multiple keywords are considered joined by
"AND".
In addition to the search parameters, there are three
"flags" that can be set in the Query object:
1. expandServices: when TRUE, this flag will cause MOBY Central
to traverse the Service ontology and discover services that
are child types (more specific) than the Service-type you
requested. For example, you might request
"alignment", and it would discover services such as
"Blast", "Smith Waterman",
"Needleman Wunsch".
2. expandObjects: when TRUE, this flag will cause MOBY Central to
traverse the Class ontology to find services that operate not
only on the Object Class you are querying, but also any
ontolological parent types of that Object Class. For example,
if you request services that work on AnnotatedSequence Objects
this flag will also return services that work on Sequence
objects, since AnnotatedSequence objects inherit from Sequence
objects.
3. authoritative: When this boolean flag is TRUE, only services
that report themselves to be "authoritative" for a
particular transformation will be discovered. When set to any
other value both authoritative and non-authoritative services
will be discovered.
The Query object structure is as follows:
<inputObjects>
<Input>
<!-- one or more Simple or Collection articles -->
</Input>
</inputObjects>
<outputObjects>
<Output>
<!-- one or more Simple or Collection articles -->
</Output>
</outputObjects>
<serviceType>ServiceTypeTerm</serviceType>
<Protocol>moby</Protocol>
<authURI>desired.service.provider</authURI>;
<serviceName>MyServiceName</serviceName>;
<expandObjects>1|0</expandObjects>
<expandServices>1|0</expandServices>
<authoritative>1|0</authoritative>
<keywords>
<keyword>something</keyword>
....
....
</keywords>
<Services>
<Service authURI="authority.URI.here" serviceName="MyService" lsid='urn:lsid:authority.uri:serviceinstance:id'>
<serviceType lsid='urn:lsid:authority.uri:servicetype:OntologyTerm'>Ontology_Term</serviceType>
<authoritative>1</authoritative>
<Category>moby</Category> <!-- 'moby' or 'cgi' or 'soap' -->
<Description><![CDATA[free text description here]]></Description>
<contactEmail>your@email.addy.here</contactEmail>
<URL>http://service.endpoint.here/scriptname</URL>
<Input>
<!-- zero or more Simple and/or Collection articles -->
</Input>
<Output>
<!-- zero or more Simple and/or Collection articles -->
</Output>
<secondaryArticles>
<!-- zero or more Secondary (Parameter) articles -->
</secondaryArticles>
</Service>
...
<!-- one or more Service blocks may be returned -->
...
...
</Services>
String retrieveService(String query)
query - a string of XML similar to the following
<retrieveService>
<Service authURI="authority.URI.here" serviceName="MyService"/>
<retrieveService>
Note: AuthURI and serviceName attributes are sufficient
to identify a unique service, and both are required in the element.
* moby
<Service authURI="authority.URI.here" serviceName="MyService" lsid='urn:lsid:authority.uri:serviceinstance:id'>
<![CDATA[WSDL document here]]
</Service>
* cgi
<Service>
<serviceName>NameOfService</serviceName>
<URL>http://service.url.here</URL>;
<GETstring>sprintf_formatted_GET_string</GETstring>
<Description>
<![CDATA[human readable description here]]>
</Description>
</Service>
* soap
UNKNOWN AT THIS TIME
Note: The WSDL that is returned is not currently valid.
It will only become valid once we have the ability to convert our class
ontology into an XML schema. In addition, the WSDL that is returned does
not necessarily describe the actual interface of the service. In the
BioMOBY system, you are allowed to pass more complex objects to a
service, and the service is allowed to pass more complex objects back to
you, so long as they obey the parentage rules of the class ontology. As
such, the WSDL that you receive is the minimal interface for the service,
not necessarily the actual interface.
The use of WSDL in the BioMOBY system is subject to change in future
revisions, and is provided at this time only to facilitate the creation
of service stubs on the client side using the commonly available WSDL
parsersString retrieveResourceURLs()
<resourceURLs>
<Resource name="ServiceInstance" url="http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances>
<Resource name="Object" url="http://biomoby.org/RESOURCES/MOBY-S/Objects"/>
<Resource name="Namespace" url="http://biomoby.org/RESOURCES/MOBY-S/Namespaces"/>
<Resource name="Service" url="http://biomoby.org/RESOURCES/MOBY-S/Services/Services"/>
<Resource name="Full" url="http://biomoby.org/RESOURCES/MOBY-S/Services/FULL"/>
</resourceURLs>
Note: Finds the URL from which the RDF of a MOBY
Ontology can be retrieved by HTTP GET. There are five possible ontology
names: "Service", "Object", "Namespace", "ServiceInstance", or "Full"
(Full retrieves all of the ontologies)String retrieveServiceProviders()
<serviceTypes>
<serviceType name="serviceName" lsid='urn:lsid:authority.uri:servicetype:id'>
<Description><![CDATA[free text description here]]></Description>
<contactEmail>email@address here</contactEmail>
<authURI>authority.uri.here</authURI>
</serviceType>
...
</serviceTypes>
String retrieveServiceNames()
<serviceNames>
<serviceName name="serviceName" authURI='authority.info.here' lsid='urn:lsid:authority.uri:namespace:id'/>
...
</serviceNames>
String retrieveServiceTypes()
<serviceTypes>
<serviceType name="serviceName" lsid='urn:lsid:authority.uri:servicetype:id'>
<Description><![CDATA[free text description here]]></Description>
<contactEmail>email@address here</contactEmail>
<authURI>authority.uri.here</authURI>
</serviceType>
...
</serviceTypes>
String retrieveObjectNames()
<objectNames>
<Object name="objectName" lsid='urn:lsid:authority.uri:namespace:id'>
<Description><![CDATA[free text description here]]></Description>
</Object>
...
</objectNames>
String retrieveObjectDefinitions(String query)
query - input XML, for example:
<retrieveObjectDefinition>
<objectType>ExistingObjectClassname</objectType>
</retrieveObjectDefinition>
<retrieveObjectDefinition>
<objectType lsid='urn:lsid:authority.uri:namespace:id'>ObjectClassName</objectType>
<Description><![CDATA[
human readable description
of data type]]>
</Description>
<Relationship relationshipType="RelationshipOntologyTerm"
lsid='urn:lsid:authority.uri:namespace:id'>
<objectType articleName="SomeName" lsid='urn:lsid:authority.uri:namespace:id'>ExistingObjectType</objectType>
</Relationship>
...
<authURI>owner.URI.here</authURI>
<contactEmail>owner@their.address.com</contactEmail>
</retrieveObjectDefinition>
String retrieveNamespaces()
<Namespaces>
<Namespace name="namespace" lsid='urn:lsid:authority.uri:namespace:id'>
<Description><![CDATA[free text description here]]></Description>
<contactEmail>email@address here</contactEmail>
<authURI>authority.uri.here</authURI>
</Namespace>
...
</Namespaces>
String retrieveObjectSchema(String query)
query - a string of XML, for example:
<retrieveObjectSchema>
<objectType>ObjectType | all</objectType>
</retrieveObjectSchema>
<Objects>
<Object name="ObjectOntologyTerm" lsid='urn:lsid:authority.uri:namespace:id'>
<Schema><![CDATA[
<XSD schema here>]]>
</Schema>
</Object>
...
</Objects>
String Relationships(String query)
query - a string of XML, for example:
<Relationship>
[ <objectType>OntologyTerm</objectType> |
<serviceType>OntologyTerm</serviceType> ]
<relationshipType>RelationshipOntologyTerm1</relationshipType>
<relationshipType>RelationshipOntologyTerm2</relationshipType>
...
<expandRelationship>1|0</expandRelationship>
<Relationship>
<Relationships>
<Relationship relationshipType="RelationshipOntologyTerm1"
lsid='urn:lsid:authority.uri:namespace:id'>
[ <objecctType lsid='...' articleName='foo'>OntologyTerm</objectType> |
<serviceType lsid='...'>OntologyTerm</serviceType> ]
...
</Relationship>
...
</Relationships>
Note: Unless the expandRelationships flag is set, it
will return only the first-level objects in that relationship (i.e. take
one step up the Ontology hierarchy). If the flag is set, MOBY Central
will traverse the ontology right back to its root as a flattened list
|
Version: 1.1.1 | |||||||||
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