org.openprovenance.elmo
Class RdfOPMFactory

java.lang.Object
  org.openprovenance.model.OPMFactory
      org.openprovenance.elmo.RdfOPMFactory

All Implemented Interfaces:

CommonURIs

public class RdfOPMFactory
extends OPMFactory

The factory class to create OPM entities that can be serialised to rdf. This package relies on Sesame's elmo, which uses a facade object to access the content of the triple store and update it. Each OPM class generated by JAXB is subclassed to get access to the facade for each instance. The factory class offers several kinds of factory methods. - factory methods that are inherited from OPMFactory, created instance of objects with a facade to the triple store. - factory methods that clone opm entities and create new instances with a facade to a triple store - factroy methods that create facade-with instances of OPM classes from the content of a triple store. Note that to ensure that graph structure is preserved between the Java representation and the RDF triple store, an instance of this factory class is stateful! (The original OPMFactory was purely stateless. Note that JAXB beans that have a field that contains a list only offer a getter method for these fields. They can be updated by getting the list and updating it. If bean content are update this way, the RDF facade may not be aware of the update, and may not propagate it to the triple store. Therefore the factory classes (OPMFactory) offers a number of update methods (typically to add new elements to lists). These methods are overridden by RdfOPMFactory to update the triple store.

Field Summary

Fields inherited from class org.openprovenance.model.OPMFactory

builder, compactId, dataFactory, of, opmGraphIdPrefix, packageList, roleIdPrefix, usedIdPrefix, wasControlledByIdPrefix, wasDerivedFromIdPrefix, wasGenerateByIdPrefix, wasTriggeredByIdPrefix

Fields inherited from interface org.openprovenance.model.CommonURIs

ENCODING_PROPERTY, LABEL_PROPERTY, NEW_ENCODING_PROPERTY, NEW_LABEL_PROPERTY, NEW_PNAME_PROPERTY, NEW_PROFILE_PROPERTY, NEW_TYPE_PROPERTY, NEW_VALUE_PROPERTY, PNAME_PROPERTY, PROFILE_PROPERTY, TYPE_PROPERTY, VALUE_PROPERTY

Constructor Summary

RdfOPMFactory(ObjectFactory o)

RdfOPMFactory(ObjectFactory o, org.openrdf.elmo.ElmoManager manager)

Method Summary

void	addAccounts(AnnotationOrEdgeOrNode hasAccounts, List<AccountRef> accounts)
void	addAccounts(HasAccounts element, Collection<AccountRef> accounts)
void	addAnnotation(Annotable annotable, Annotation ann)
void	addAnnotation(Annotable annotable, EmbeddedAnnotation ann) Add annotation to an annotable JAXB Bean and its corresponding RDF facade.
void	addAnnotation(Annotable annotable, javax.xml.bind.JAXBElement<? extends EmbeddedAnnotation> ann)
void	addAnnotation(Annotable annotable, Label ann)
void	addAnnotation(Annotable annotable, Type ann)
void	addAnnotation(Annotable annotable, Value ann)
void	addNewAnnotations(Annotable res, List<javax.xml.bind.JAXBElement<? extends EmbeddedAnnotation>> anns)
void	addProperty(Annotation ann, Property p)
void	addProperty(EmbeddedAnnotation ann, Property p)
String	autoGenerateId(String prefix) By default, no auto generation of Id.
String	autoGenerateId(String prefix, String id) Conditional autogeneration of Id.
Object	getFromRegisters(String id)
RdfAccount	newAccount(Account a)
RdfAccount	newAccount(QName qname)
List<AccountRef>	newAccounts(List<AccountRef> accounts)
RdfAgent	newAgent(Agent a)
RdfAgent	newAgent(QName qname)
RdfAnnotation	newAnnotation(Annotation a)
Annotation	newAnnotation(Annotation ann)
RdfArtifact	newArtifact(Artifact a)
RdfArtifact	newArtifact(QName qname)
RdfEmbeddedAnnotation	newEmbeddedAnnotation(Annotation a)
OPMGraph	newOPMGraph(OPMGraph gr)
RdfOPMGraph	newOPMGraph(OPMGraph gr) Clones an OPMGraph to an OPMGraph with facade, and creates corresponding rdf representation in triple store.
OPMGraph	newOPMGraph(String id, Collection<Account> accs, Collection<Overlaps> ops, Collection<Process> ps, Collection<Artifact> as, Collection<Agent> ags, Collection<Object> lks, Collection<Annotation> anns)
RdfOTime	newOTime(OTime a)
RdfProcess	newProcess(Process a)
RdfProcess	newProcess(QName qname)
List<Property>	newProperties(List<Property> props)
RdfProperty	newProperty(Property a)
RdfRole	newRole(QName qname)
RdfRole	newRole(Role r)
RdfUsed	newUsed(Used a)
Used	newUsed(Used d)
RdfWasControlledBy	newWasControlledBy(WasControlledBy a)
WasControlledBy	newWasControlledBy(WasControlledBy d)
RdfWasDerivedFrom	newWasDerivedFrom(WasDerivedFrom a)
WasDerivedFrom	newWasDerivedFrom(WasDerivedFrom d)
RdfWasGeneratedBy	newWasGeneratedBy(WasGeneratedBy a)
WasGeneratedBy	newWasGeneratedBy(WasGeneratedBy d)
RdfWasTriggeredBy	newWasTriggeredBy(WasTriggeredBy a)
WasTriggeredBy	newWasTriggeredBy(WasTriggeredBy d)
void	processAnnotations(Annotable a, Annotable res)
RdfAccount	register(QName qname, RdfAccount account)
RdfAgent	register(QName qname, RdfAgent agent)
RdfArtifact	register(QName qname, RdfArtifact artifact)
RdfProcess	register(QName qname, RdfProcess process)
Account	register(String id, Account account)
Agent	register(String id, Agent agent)
Artifact	register(String id, Artifact artifact)
Process	register(String id, Process process)

Methods inherited from class org.openprovenance.model.OPMFactory

addAccounts, addAnnotation, addAnnotation, addAnnotation, addAnnotations, addCompactAnnotation, addProperty, addProperty, addValue, compactAnnotation, expandAnnotation, getEncoding, getFactory, getLabel, getLabel, getLabel, getLabels, getObjectFactory, getPackageList, getPname, getPname, getPname, getPnames, getProfile, getProfile, getProfile, getProfiles, getRole, getType, getType, getType, getTypes, getValue, getValue, getValues, newAccount, newAccount, newAccount, newAccountRef, newAccounts, newAgent, newAgent, newAgent, newAgentRef, newAnnotation, newAnnotation, newAnnotation, newAnnotation, newAnnotation, newAnnotation, newAnnotation, newAnnotation, newAnnotation, newAnnotation, newAnnotation, newAnnotationRef, newArtifact, newArtifact, newArtifact, newArtifactRef, newCausalDependencyRef, newCausalDependencyRef, newCausalDependencyRef, newCausalDependencyRef, newCausalDependencyRef, newEmbeddedAnnotation, newEmbeddedAnnotation, newEmbeddedAnnotation, newInstantaneousTime, newInstantaneousTime, newInstantaneousTime, newInstantaneousTimeNow, newLabel, newOPMGraph, newOPMGraph, newOPMGraph, newOPMGraph, newOPMGraph, newOPMGraph, newOPMGraph, newOTime, newOTime, newOTime, newOTime, newOTime, newOTime, newOTime, newOverlaps, newOverlaps, newPName, newProcess, newProcess, newProcess, newProcessRef, newProfile, newProperty, newProperty, newRole, newRole, newRole, newRoleRef, newType, newUsed, newUsed, newUsed, newUsed, newUsedStar, newUsedStar, newValue, newWasControlledBy, newWasControlledBy, newWasControlledBy, newWasControlledBy, newWasControlledBy, newWasDerivedFrom, newWasDerivedFrom, newWasDerivedFrom, newWasDerivedFrom, newWasDerivedFromStar, newWasDerivedFromStar, newWasGeneratedBy, newWasGeneratedBy, newWasGeneratedBy, newWasGeneratedBy, newWasGeneratedByStar, newWasGeneratedByStar, newWasTriggeredBy, newWasTriggeredBy, newWasTriggeredBy, newWasTriggeredBy, newWasTriggeredByStar, newWasTriggeredByStar, newXMLGregorianCalendar, setIdForCompactAnnotation

Methods inherited from class java.lang.Object

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

Constructor Detail

RdfOPMFactory

public RdfOPMFactory(ObjectFactory o)

RdfOPMFactory

public RdfOPMFactory(ObjectFactory o,
                     org.openrdf.elmo.ElmoManager manager)

Method Detail

autoGenerateId

public String autoGenerateId(String prefix)

Description copied from class: OPMFactory

By default, no auto generation of Id. Override this behaviour if required.

Overrides:

autoGenerateId in class OPMFactory

autoGenerateId

public String autoGenerateId(String prefix,
                             String id)

Description copied from class: OPMFactory

Conditional autogeneration of Id. By default, no auto generation of Id. Override this behaviour if required.

Overrides:

autoGenerateId in class OPMFactory

addProperty

public void addProperty(EmbeddedAnnotation ann,
                        Property p)

Overrides:

addProperty in class OPMFactory

addProperty

public void addProperty(Annotation ann,
                        Property p)

Overrides:

addProperty in class OPMFactory

addAccounts

public void addAccounts(HasAccounts element,
                        Collection<AccountRef> accounts)

Overrides:

addAccounts in class OPMFactory

addAnnotation

public void addAnnotation(Annotable annotable,
                          javax.xml.bind.JAXBElement<? extends EmbeddedAnnotation> ann)

Overrides:

addAnnotation in class OPMFactory

addAnnotation

public void addAnnotation(Annotable annotable,
                          Label ann)

Overrides:

addAnnotation in class OPMFactory

addAnnotation

public void addAnnotation(Annotable annotable,
                          Type ann)

addAnnotation

public void addAnnotation(Annotable annotable,
                          Value ann)

Overrides:

addAnnotation in class OPMFactory

addAnnotation

public void addAnnotation(Annotable annotable,
                          Annotation ann)

addAnnotation

public void addAnnotation(Annotable annotable,
                          EmbeddedAnnotation ann)

Add annotation to an annotable JAXB Bean and its corresponding RDF facade.

Overrides:

addAnnotation in class OPMFactory

newOPMGraph

public OPMGraph newOPMGraph(String id,
                            Collection<Account> accs,
                            Collection<Overlaps> ops,
                            Collection<Process> ps,
                            Collection<Artifact> as,
                            Collection<Agent> ags,
                            Collection<Object> lks,
                            Collection<Annotation> anns)

Overrides:

newOPMGraph in class OPMFactory

newArtifact

public RdfArtifact newArtifact(Artifact a)

newArtifact

public RdfArtifact newArtifact(QName qname)

newProcess

public RdfProcess newProcess(Process a)

newProcess

public RdfProcess newProcess(QName qname)

newAgent

public RdfAgent newAgent(Agent a)

newAgent

public RdfAgent newAgent(QName qname)

newAccount

public RdfAccount newAccount(QName qname)

newAccount

public RdfAccount newAccount(Account a)

newRole

public RdfRole newRole(QName qname)

newRole

public RdfRole newRole(Role r)

newProperty

public RdfProperty newProperty(Property a)

newAnnotation

public RdfAnnotation newAnnotation(Annotation a)

newEmbeddedAnnotation

public RdfEmbeddedAnnotation newEmbeddedAnnotation(Annotation a)

register

public RdfAgent register(QName qname,
                         RdfAgent agent)

register

public RdfProcess register(QName qname,
                           RdfProcess process)

register

public RdfArtifact register(QName qname,
                            RdfArtifact artifact)

register

public RdfAccount register(QName qname,
                           RdfAccount account)

register

public Agent register(String id,
                      Agent agent)

register

public Process register(String id,
                        Process process)

register

public Artifact register(String id,
                         Artifact artifact)

register

public Account register(String id,
                        Account account)

newOTime

public RdfOTime newOTime(OTime a)

addAccounts

public void addAccounts(AnnotationOrEdgeOrNode hasAccounts,
                        List<AccountRef> accounts)

newAccounts

public List<AccountRef> newAccounts(List<AccountRef> accounts)

newWasDerivedFrom

public RdfWasDerivedFrom newWasDerivedFrom(WasDerivedFrom a)

newWasGeneratedBy

public RdfWasGeneratedBy newWasGeneratedBy(WasGeneratedBy a)

newUsed

public RdfUsed newUsed(Used a)

newWasControlledBy

public RdfWasControlledBy newWasControlledBy(WasControlledBy a)

newWasTriggeredBy

public RdfWasTriggeredBy newWasTriggeredBy(WasTriggeredBy a)

processAnnotations

public void processAnnotations(Annotable a,
                               Annotable res)

addNewAnnotations

public void addNewAnnotations(Annotable res,
                              List<javax.xml.bind.JAXBElement<? extends EmbeddedAnnotation>> anns)

Overrides:

addNewAnnotations in class OPMFactory

newOPMGraph

public OPMGraph newOPMGraph(OPMGraph gr)

newWasDerivedFrom

public WasDerivedFrom newWasDerivedFrom(WasDerivedFrom d)

Overrides:

newWasDerivedFrom in class OPMFactory

newWasTriggeredBy

public WasTriggeredBy newWasTriggeredBy(WasTriggeredBy d)

Overrides:

newWasTriggeredBy in class OPMFactory

newUsed

public Used newUsed(Used d)

Overrides:

newUsed in class OPMFactory

newWasGeneratedBy

public WasGeneratedBy newWasGeneratedBy(WasGeneratedBy d)

Overrides:

newWasGeneratedBy in class OPMFactory

newWasControlledBy

public WasControlledBy newWasControlledBy(WasControlledBy d)

Overrides:

newWasControlledBy in class OPMFactory

newProperties

public List<Property> newProperties(List<Property> props)

newAnnotation

public Annotation newAnnotation(Annotation ann)

Overrides:

newAnnotation in class OPMFactory

getFromRegisters

public Object getFromRegisters(String id)

newOPMGraph

public RdfOPMGraph newOPMGraph(OPMGraph gr)

Clones an OPMGraph to an OPMGraph with facade, and creates corresponding rdf representation in triple store. This is definitely a stateful operation.

Overrides:

newOPMGraph in class OPMFactory