eu.transformproject.provenance.storage

Class ProvenancePersistenceManager

java.lang.Object

eu.transformproject.provenance.storage.ProvenancePersistenceManager

All Implemented Interfaces:

ProvenanceStorageInterface

public class ProvenancePersistenceManager
extends java.lang.Object
implements ProvenanceStorageInterface

This class contains a set of methods for provenance data storage. It uses hibernate technologies to implement the ProvenanceStorageInterface.

Author:

Roxana Ma. Danger Mercaderes

Constructor Summary

Constructors

Constructor and Description
ProvenancePersistenceManager(ProvenanceServer provenanceServer)

Method Summary

Methods

Modifier and Type	Method and Description
java.lang.String	addAnnotation(OPMEntity subjectEntity, Property prop, java.lang.String value)
java.lang.String	addAnnotation(OPMEntity entity, java.lang.String owl_prop, java.lang.String value)
java.lang.String	addAnnotation(java.lang.String uriEntityOrDependence, java.lang.String owl_prop, java.lang.String value) Adds an annotation to an entity or a dependence, owl_prop is the property to annotate which must appear in the ontology profile (or set of domain-user ontologies) associated to the server, the value associated to the property is value.
java.lang.String[]	addAnnotations(java.lang.String uriEntityOrDependence, AnnotationSet annotations)
OPMDependence	addCausalDependence(OPMEntityNode entityCause, OPMEntityNode entityEffect)
java.lang.String	addCausalDependence(java.lang.String uriEntityCause, java.lang.String uriEntityDest) As the previous method but the causal dependences to create must correspond with one of the five defined in \cite{Moreau2010}.
java.lang.String	addCausalDependence(java.lang.String uriEntityCause, java.lang.String opmo_dependenceClass, java.lang.String uriEntityDest) Defines a causal dependence from the entity uriEntityDest to uriEntityCause in the graph idGraph.
java.lang.Object[]	addOPMEntityToGraph(OPMGraph g, OPMEntity entity)
void	associateToAccount(java.lang.String uriEntity, java.lang.String uriAccount) Specify an account for which an specific OPM entity can be viewed.
void	closeSession()
AnnotationSet	composeAnnotation(java.lang.String owl_prop, java.lang.String value) Create an AnnotationSet object, initialising it with the annotation defined by the pair: owl_prop, value.
OPMDependence	createCausalDependence(OPMEntityNode entityCause, OPMEntityNode entityEffect)
void	endProcess(java.lang.String processUri) Allows to store the date-time in which a process has finalised.
void	endProcessWithStatus(java.lang.String processUri, java.lang.String processStatus) Allows to store the date-time in which a process has finalised together with its status.
java.util.List	executeSQL(java.lang.String sql)
void	finalize()
<T> T	find(java.lang.Class<T> clazz, long primaryKey)
java.lang.Object	flushAndRefresh(java.lang.Object o)
java.util.Collection<? extends java.lang.String>	getColsOfTables(java.lang.String tname)
OPMGraph	getCurrGraph()
java.lang.String	getEntityURI(EntityType et, AnnotationSet annotations)
java.lang.String	getEntityURI(java.lang.String owl_opm_Class, AnnotationSet annotations) Generate or retrieve an URI associated to the given parameters.
long	getKeyFromURI(java.lang.String uri)
OPMEntity	getOPMEntity(long key)
OPMEntity	getOPMEntity(java.lang.String entityURI) Recover an OPMEntity given its URI.
OPMEntity	getOPMEntityWithValue(java.lang.String value)
java.lang.String	getOPMGraphForProject(java.lang.String projectName) If it exists a graph associated to this project name, this method returns it, otherwise, it creates a new graph, and adds to it an annotation associating it with a project.
OPMGraph	getOPMGraphViewForEntities(java.util.HashSet<java.lang.String> entityURIs, int pathlenght)
OPMGraph	getOPMGraphViewForEntities(java.util.HashSet<java.lang.String> entityURIs, int pathlenght, java.util.HashMap<java.lang.String,java.lang.Object> cloneMap)
ProcessStatus	getProcessStatus(java.lang.String processStatus)
java.lang.String	getProjectNameOfEntity(java.lang.String entityURI)
Property	getProperty(java.lang.String prop)
java.util.Date	getSyncTime()
java.lang.String	getTableNameForColumn(java.lang.String col)
java.lang.String	getURI(long key)
java.lang.String	getURI(OPMDependenceType depType)
java.lang.String	getURI(OPMEntity entity)
java.lang.String	getURI(OPMEntityType entityType)
java.lang.String	newGraph() Adds a new graph in the provenance store.
void	openSession()
java.lang.Object[]	openSession(java.lang.Object[] deAttachObjects)
void	setCurrentGraph(java.lang.String uriGraph) Specify that all the new entity definitions belong to the OPM graph with URI idGraph.
void	setId(java.lang.String entityURI, java.lang.String newId)
void	setOntologies(Ontologies ontos)
void	setProcessEndAt(java.lang.String processUri, java.util.Date timeEnd)
void	setProcessStartAt(java.lang.String processUri, java.util.Date timeStart)
void	setProcessStatus(java.lang.String processUri, java.lang.String processStatus) Allows to set the status of a process.

Methods inherited from class java.lang.Object

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

Constructor Detail

ProvenancePersistenceManager

public ProvenancePersistenceManager(ProvenanceServer provenanceServer)
                             throws org.hibernate.MappingException,
                                    java.lang.Exception

Throws:

org.hibernate.MappingException

java.lang.Exception

Method Detail

openSession

public void openSession()

openSession

public java.lang.Object[] openSession(java.lang.Object[] deAttachObjects)

closeSession

public void closeSession()

find

public <T> T find(java.lang.Class<T> clazz,
         long primaryKey)

flushAndRefresh

public java.lang.Object flushAndRefresh(java.lang.Object o)
                                 throws java.lang.Exception

Specified by:

flushAndRefresh in interface ProvenanceStorageInterface

Throws:

java.lang.Exception

getURI

public java.lang.String getURI(OPMEntity entity)

getURI

public java.lang.String getURI(OPMEntityType entityType)
                        throws java.lang.Exception

Throws:

java.lang.Exception

getURI

public java.lang.String getURI(OPMDependenceType depType)
                        throws java.lang.Exception

Throws:

java.lang.Exception

getKeyFromURI

public long getKeyFromURI(java.lang.String uri)

getSyncTime

public java.util.Date getSyncTime()
                           throws java.lang.Exception

Specified by:

getSyncTime in interface ProvenanceStorageInterface

Returns:

Returns the date/time as in the time server

Throws:

java.lang.Exception

newGraph

public java.lang.String newGraph()
                          throws java.lang.Exception

Description copied from interface: ProvenanceStorageInterface

Adds a new graph in the provenance store. Returns the URI of the inserted graph.

Specified by:

newGraph in interface ProvenanceStorageInterface

Returns:

Returns the URI of a new OPM graph to be inserted in the provenance store.

Throws:

java.lang.Exception

getEntityURI

public java.lang.String getEntityURI(java.lang.String owl_opm_Class,
                            AnnotationSet annotations)
                              throws java.lang.Exception

Description copied from interface: ProvenanceStorageInterface

Generate or retrieve an URI associated to the given parameters. Given an owl_opm_class from the ontology profile (or set of domain-user ontologies) associated to the server, and a set of annotations that characterise the current entity. This method will retrieve a stored OPM entity with such features, or create a new one. The URI of the generated/created instance will be returned.

Specified by:

getEntityURI in interface ProvenanceStorageInterface

Parameters:

owl_opm_Class - class to which the opm entity belongs

annotations - annotations associated to the entity to create/retrieve

Returns:

The URI of the retrieved/created instance.

Throws:

java.lang.Exception

getEntityURI

public java.lang.String getEntityURI(EntityType et,
                            AnnotationSet annotations)
                              throws java.lang.Exception

Throws:

java.lang.Exception

addAnnotation

public java.lang.String addAnnotation(OPMEntity entity,
                             java.lang.String owl_prop,
                             java.lang.String value)
                               throws java.lang.Exception

Throws:

java.lang.Exception

associateToAccount

public void associateToAccount(java.lang.String uriEntity,
                      java.lang.String uriAccount)
                        throws java.lang.Exception

Description copied from interface: ProvenanceStorageInterface

Specify an account for which an specific OPM entity can be viewed.

Specified by:

associateToAccount in interface ProvenanceStorageInterface

Parameters:

uriEntity - OPM entity URI of the entity to associate to the account

uriAccount - OPM Account URI for the OPM entity.

Throws:

java.lang.Exception

addCausalDependence

public java.lang.String addCausalDependence(java.lang.String uriEntityCause,
                                   java.lang.String opmo_dependenceClass,
                                   java.lang.String uriEntityDest)
                                     throws java.lang.Exception

Description copied from interface: ProvenanceStorageInterface

Defines a causal dependence from the entity uriEntityDest to uriEntityCause in the graph idGraph. opmo_dependenceClass should correspond with a class derived from opmo:Edge, defined in the ontology profile (or set of domain-user ontologies) associated to the server.

Specified by:

addCausalDependence in interface ProvenanceStorageInterface

Returns:

Throws:

java.lang.Exception

addCausalDependence

public java.lang.String addCausalDependence(java.lang.String uriEntityCause,
                                   java.lang.String uriEntityDest)
                                     throws java.lang.Exception

Description copied from interface: ProvenanceStorageInterface

As the previous method but the causal dependences to create must correspond with one of the five defined in \cite{Moreau2010}.

Specified by:

addCausalDependence in interface ProvenanceStorageInterface

Returns:

Throws:

java.lang.Exception

addCausalDependence

public OPMDependence addCausalDependence(OPMEntityNode entityCause,
                                OPMEntityNode entityEffect)
                                  throws java.lang.Exception

Throws:

java.lang.Exception

setOntologies

public void setOntologies(Ontologies ontos)

getProperty

public Property getProperty(java.lang.String prop)
                     throws java.lang.Exception

Throws:

java.lang.Exception

getOPMEntityWithValue

public OPMEntity getOPMEntityWithValue(java.lang.String value)

addAnnotation

public java.lang.String addAnnotation(java.lang.String uriEntityOrDependence,
                             java.lang.String owl_prop,
                             java.lang.String value)
                               throws java.lang.Exception

Description copied from interface: ProvenanceStorageInterface

Adds an annotation to an entity or a dependence, owl_prop is the property to annotate which must appear in the ontology profile (or set of domain-user ontologies) associated to the server, the value associated to the property is value.

Specified by:

addAnnotation in interface ProvenanceStorageInterface

Returns:

Throws:

java.lang.Exception

addAnnotation

public java.lang.String addAnnotation(OPMEntity subjectEntity,
                             Property prop,
                             java.lang.String value)
                               throws java.lang.Exception

Throws:

java.lang.Exception

addAnnotations

public java.lang.String[] addAnnotations(java.lang.String uriEntityOrDependence,
                                AnnotationSet annotations)
                                  throws java.lang.Exception

Specified by:

addAnnotations in interface ProvenanceStorageInterface

Throws:

java.lang.Exception

executeSQL

public java.util.List executeSQL(java.lang.String sql)

setCurrentGraph

public void setCurrentGraph(java.lang.String uriGraph)
                     throws java.lang.Exception

Description copied from interface: ProvenanceStorageInterface

Specify that all the new entity definitions belong to the OPM graph with URI idGraph.

Specified by:

setCurrentGraph in interface ProvenanceStorageInterface

Parameters:

uriGraph - URI of the graph for all new declared entities.

Throws:

java.lang.Exception

getOPMGraphForProject

public java.lang.String getOPMGraphForProject(java.lang.String projectName)
                                       throws java.lang.Exception

Description copied from interface: ProvenanceStorageInterface

If it exists a graph associated to this project name, this method returns it, otherwise, it creates a new graph, and adds to it an annotation associating it with a project.

Specified by:

getOPMGraphForProject in interface ProvenanceStorageInterface

Parameters:

projectName - name of the project described by the created graph.

Returns:

Throws:

java.lang.Exception

getProjectNameOfEntity

public java.lang.String getProjectNameOfEntity(java.lang.String entityURI)
                                        throws java.lang.Exception

Throws:

java.lang.Exception

endProcess

public void endProcess(java.lang.String processUri)
                throws java.lang.Exception

Description copied from interface: ProvenanceStorageInterface

Allows to store the date-time in which a process has finalised.

Specified by:

endProcess in interface ProvenanceStorageInterface

Parameters:

processUri - the process that has finished

Throws:

java.lang.Exception

getProcessStatus

public ProcessStatus getProcessStatus(java.lang.String processStatus)
                               throws java.lang.Exception

Throws:

java.lang.Exception

endProcessWithStatus

public void endProcessWithStatus(java.lang.String processUri,
                        java.lang.String processStatus)
                          throws java.lang.Exception

Description copied from interface: ProvenanceStorageInterface

Allows to store the date-time in which a process has finalised together with its status.

Specified by:

endProcessWithStatus in interface ProvenanceStorageInterface

Parameters:

processUri - the process that has finished

processStatus - status of the process that has finished

Throws:

java.lang.Exception

setProcessStartAt

public void setProcessStartAt(java.lang.String processUri,
                     java.util.Date timeStart)
                       throws java.lang.Exception

Specified by:

setProcessStartAt in interface ProvenanceStorageInterface

Throws:

java.lang.Exception

setProcessEndAt

public void setProcessEndAt(java.lang.String processUri,
                   java.util.Date timeEnd)
                     throws java.lang.Exception

Specified by:

setProcessEndAt in interface ProvenanceStorageInterface

Throws:

java.lang.Exception

composeAnnotation

public AnnotationSet composeAnnotation(java.lang.String owl_prop,
                              java.lang.String value)
                                throws java.lang.Exception

Description copied from interface: ProvenanceStorageInterface

Create an AnnotationSet object, initialising it with the annotation defined by the pair: owl_prop, value.

Specified by:

composeAnnotation in interface ProvenanceStorageInterface

Returns:

Throws:

java.lang.Exception

setProcessStatus

public void setProcessStatus(java.lang.String processUri,
                    java.lang.String processStatus)
                      throws java.lang.Exception

Description copied from interface: ProvenanceStorageInterface

Allows to set the status of a process.

Specified by:

setProcessStatus in interface ProvenanceStorageInterface

processStatus - string representing the status of a process. Only the current status of a process is maintained. In future versions, other status annotations would be maintained at different times.

Throws:

java.lang.Exception

getCurrGraph

public OPMGraph getCurrGraph()
                      throws java.lang.Exception

Specified by:

getCurrGraph in interface ProvenanceStorageInterface

Throws:

java.lang.Exception

getOPMEntity

public OPMEntity getOPMEntity(java.lang.String entityURI)
                       throws java.lang.Exception

Description copied from interface: ProvenanceStorageInterface

Recover an OPMEntity given its URI.

Specified by:

getOPMEntity in interface ProvenanceStorageInterface

Parameters:

entityURI - URI of the entity to recover.

Returns:

Throws:

java.lang.Exception

setId

public void setId(java.lang.String entityURI,
         java.lang.String newId)
           throws java.lang.Exception

Throws:

java.lang.Exception

getOPMEntity

public OPMEntity getOPMEntity(long key)

getURI

public java.lang.String getURI(long key)

getTableNameForColumn

public java.lang.String getTableNameForColumn(java.lang.String col)

getColsOfTables

public java.util.Collection<? extends java.lang.String> getColsOfTables(java.lang.String tname)

finalize

public void finalize()
              throws java.sql.SQLException

Overrides:

finalize in class java.lang.Object

Throws:

java.sql.SQLException

createCausalDependence

public OPMDependence createCausalDependence(OPMEntityNode entityCause,
                                   OPMEntityNode entityEffect)
                                     throws java.lang.Exception

Throws:

java.lang.Exception

getOPMGraphViewForEntities

public OPMGraph getOPMGraphViewForEntities(java.util.HashSet<java.lang.String> entityURIs,
                                  int pathlenght)
                                    throws java.lang.Exception

Throws:

java.lang.Exception

getOPMGraphViewForEntities

public OPMGraph getOPMGraphViewForEntities(java.util.HashSet<java.lang.String> entityURIs,
                                  int pathlenght,
                                  java.util.HashMap<java.lang.String,java.lang.Object> cloneMap)
                                    throws java.lang.Exception

Throws:

java.lang.Exception

addOPMEntityToGraph

public java.lang.Object[] addOPMEntityToGraph(OPMGraph g,
                                     OPMEntity entity)
                                       throws java.lang.Exception

Throws:

java.lang.Exception