org.biomoby.registry.Central
Class CentralImpl

java.lang.Object
  org.biomoby.registry.Central.CentralImpl

All Implemented Interfaces:

Central

public class CentralImpl
extends Object
implements Central

Author:

Eddie created Dec 21, 2005

Constructor Summary

CentralImpl()

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.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

CentralImpl

public CentralImpl()

Method Detail

findService

public String findService(String serviceQueryObject)

Description copied from interface: Central

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.

Specified by:

findService in interface Central

Parameters:

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>     
 

Returns:

a string containing the XML for the Service List response whichis as follows:

                               <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>
 

retrieveService

public String retrieveService(String query)

Description copied from interface: Central

Retrieve the definition for a service instance, as specified in WSDL format. This information is used by the client to compose queries.

Specified by:

retrieveService in interface Central

Parameters:

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.

Returns:

a string of XML, for example

                            *  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 parsers

retrieveResourceURLs

public String retrieveResourceURLs()

Description copied from interface: Central

Retrieve the URLs of all registered services.

Specified by:

retrieveResourceURLs in interface Central

Returns:

a string of XML, for example

                         <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)

retrieveServiceProviders

public String retrieveServiceProviders()

Description copied from interface: Central

Retrieve the names of all registered service providers. This allows you to see what sites are providing MOBY services.

Specified by:

retrieveServiceProviders in interface Central

Returns:

a string of output XML, for example:

                             <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>
 

retrieveServiceNames

public String retrieveServiceNames()

Description copied from interface: Central

Retrieve the names of all registered services. The service name, service provider and service lsid are all returned.

Specified by:

retrieveServiceNames in interface Central

Returns:

a string of output XML, for example:

                             <serviceNames>
                               <serviceName name="serviceName" authURI='authority.info.here' lsid='urn:lsid:authority.uri:namespace:id'/>
                                    ...
                            </serviceNames>
 

retrieveServiceTypes

public String retrieveServiceTypes()

Description copied from interface: Central

Retrieve the definitions and registration details of all registered service types.

Specified by:

retrieveServiceTypes in interface Central

Returns:

a string of output XML, for example:

                           <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>
                        
 

retrieveObjectNames

public String retrieveObjectNames()

Description copied from interface: Central

Retrieve the definitions and registration details of all registered object types.

Specified by:

retrieveObjectNames in interface Central

Returns:

a string of output XML, for example:

                          <objectNames>
                             <Object name="objectName" lsid='urn:lsid:authority.uri:namespace:id'>
                                    <Description><![CDATA[free text description here]]></Description>
                             </Object>
                                  ...
                          </objectNames>
 

retrieveObjectDefinitions

public String retrieveObjectDefinitions(String query)

Description copied from interface: Central

Retrieve the class definition, in the form of the full registration details for the class type specified by the input XML.

Specified by:

retrieveObjectDefinitions in interface Central

Parameters:

query - input XML, for example:

                       <retrieveObjectDefinition>
                            <objectType>ExistingObjectClassname</objectType>
                       </retrieveObjectDefinition>
                        
 

Returns:

a string of XML that represents the full declaration of the object, as defined by the XML used to register it. For example:

                         <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>
 

retrieveNamespaces

public String retrieveNamespaces()

Description copied from interface: Central

Retrieve a list of all registered namespaces

Specified by:

retrieveNamespaces in interface Central

Returns:

a string of XML, for example:

                        <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>
 

retrieveObjectSchema

public String retrieveObjectSchema(String query)

Description copied from interface: Central

Retrieve an XML schema representation of a particular object class. This is currently not implemented since it appears to be impossible to represent MOBY Objects in XML Schema due to limitations of XML Schema

Specified by:

retrieveObjectSchema in interface Central

Parameters:

query - a string of XML, for example:

                       <retrieveObjectSchema>
                          <objectType>ObjectType | all</objectType>
                       </retrieveObjectSchema>
 

Returns:

a string of XML that encapsulates the schema. For example:

                       <Objects>
                          <Object name="ObjectOntologyTerm" lsid='urn:lsid:authority.uri:namespace:id'>
                                 <Schema><![CDATA[
                                     <XSD schema here>]]>
                                 </Schema>
                          </Object>
                               ...
                       </Objects>
 

Relationships

public String Relationships(String query)

Description copied from interface: Central

Retrieve a list of MOBY object classes having a specified relationship with the given class

Specified by:

Relationships in interface Central

Parameters:

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>
 

Returns:

a string of XML, for example:

                      <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