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java.lang.Object org.biomoby.registry.Central.CentralImpl
public class CentralImpl
Constructor Summary | |
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CentralImpl()
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Method Summary | |
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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. |
Methods inherited from class java.lang.Object |
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equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public CentralImpl()
Method Detail |
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public String findService(String serviceQueryObject)
Central
findService
in interface Central
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>
public String retrieveService(String query)
Central
retrieveService
in interface Central
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 TIMENote: 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 parsers
public String retrieveResourceURLs()
Central
retrieveResourceURLs
in interface Central
<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)
public String retrieveServiceProviders()
Central
retrieveServiceProviders
in interface Central
<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>
public String retrieveServiceNames()
Central
retrieveServiceNames
in interface Central
<serviceNames> <serviceName name="serviceName" authURI='authority.info.here' lsid='urn:lsid:authority.uri:namespace:id'/> ... </serviceNames>
public String retrieveServiceTypes()
Central
retrieveServiceTypes
in interface Central
<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>
public String retrieveObjectNames()
Central
retrieveObjectNames
in interface Central
<objectNames> <Object name="objectName" lsid='urn:lsid:authority.uri:namespace:id'> <Description><![CDATA[free text description here]]></Description> </Object> ... </objectNames>
public String retrieveObjectDefinitions(String query)
Central
retrieveObjectDefinitions
in interface Central
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>
public String retrieveNamespaces()
Central
retrieveNamespaces
in interface Central
<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>
public String retrieveObjectSchema(String query)
Central
retrieveObjectSchema
in interface Central
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>
public String Relationships(String query)
Central
Relationships
in interface Central
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
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