Module prov.model

Package org.openprovenance.prov.model

Class IndexedDocument

java.lang.Object

org.openprovenance.prov.model.IndexedDocument

All Implemented Interfaces:

StatementAction

public class IndexedDocument
extends Object
implements StatementAction

This class provides a set of indexes over information contained in an Document, facilitating its navigation. Its constructor takes an Document builds an index for it. Of course, for the index to be maintained, one cannot access, say the list of edges, and mutate it. Instead, one has to use the add methods provided.

Note that code is not thread-safe. TODO: index annotation, index edges

Constructor Summary

Constructors

Constructor	Description
IndexedDocument(ProvFactory pFactory, Document doc)
IndexedDocument(ProvFactory pFactory, Document doc, boolean flatten)

Method Summary

Modifier and Type	Method	Description
ActedOnBehalfOf	add(ActedOnBehalfOf act)
Activity	add(Activity activity)
Agent	add(Agent agent)
AlternateOf	add(AlternateOf alt)
Entity	add(Entity entity)
HadMember	add(HadMember hm)
Activity	add(QualifiedName name, Activity activity)
Agent	add(QualifiedName name, Agent agent)
Entity	add(QualifiedName name, Entity entity)
SpecializationOf	add(SpecializationOf spec)
Used	add(Used used)
WasAssociatedWith	add(WasAssociatedWith waw)
WasAttributedTo	add(WasAttributedTo wat)
WasDerivedFrom	add(WasDerivedFrom wdf)
WasEndedBy	add(WasEndedBy web)
WasGeneratedBy	add(WasGeneratedBy wgb)
WasInfluencedBy	add(WasInfluencedBy winf)
WasInformedBy	add(WasInformedBy wib)
WasInvalidatedBy	add(WasInvalidatedBy wib)
WasStartedBy	add(WasStartedBy wsb)
<T extends Relation> T	add(T statement, int num, Collection<T> anonRelationCollection, HashMap<QualifiedName,Collection<T>> namedRelationMap, HashMap<QualifiedName,Collection<T>> effectRelationMap, HashMap<QualifiedName,Collection<T>> causeRelationMap)	Add an edge to the graph.
void	checkActivityUsedMap()
void	checkEntityCauseWasDerivedFromMap()
void	checkEntityWasGeneratedByMap()
void	doAction(ActedOnBehalfOf s)
void	doAction(Activity s)
void	doAction(Agent s)
void	doAction(AlternateOf s)
void	doAction(Bundle bun, ProvUtilities provUtilities)
void	doAction(DerivedByInsertionFrom s)
void	doAction(DerivedByRemovalFrom s)
void	doAction(DictionaryMembership s)
void	doAction(Entity s)
void	doAction(QualifiedAlternateOf s)
void	doAction(QualifiedHadMember s)
void	doAction(QualifiedSpecializationOf s)
void	doAction(HadMember s)
void	doAction(MentionOf s)
void	doAction(SpecializationOf s)
void	doAction(Used s)
void	doAction(WasAssociatedWith s)
void	doAction(WasAttributedTo s)
void	doAction(WasDerivedFrom s)
void	doAction(WasEndedBy s)
void	doAction(WasGeneratedBy s)
void	doAction(WasInfluencedBy s)
void	doAction(WasInformedBy s)
void	doAction(WasInvalidatedBy s)
void	doAction(WasStartedBy s)
Collection<Activity>	getActivities()
Activity	getActivity(QualifiedName name)
Agent	getAgent(QualifiedName name)
Collection<Agent>	getAgents()
Collection<Entity>	getEntities()
Entity	getEntity(QualifiedName name)
Collection<Used>	getUsed()	Return all used edges for this graph.
Collection<Used>	getUsed(Activity p)	Return all used edges with activity p as an effect.
Collection<Used>	getUsed(Entity p)	Return all used edges with entity a as a cause.
Collection<WasAssociatedWith>	getWasAssociatedWith()	Return all WasAssociatedWith edges for this graph.
Collection<WasAssociatedWith>	getWasAssociatedWith(Activity p)	Return all WasAssociatedWith edges with activity p as an effect.
Collection<WasAssociatedWith>	getWasAssociatedWith(Agent a)	Return all WasAssociatedWith edges with entity a as a cause.
Collection<WasDerivedFrom>	getWasDerivedFrom()	Return all WasDerivedFrom edges for this graph.
Collection<WasDerivedFrom>	getWasDerivedFromWithCause(Entity a)	Return all WasDerivedFrom edges with entity a as a cause.
Collection<WasDerivedFrom>	getWasDerivedFromWithEffect(Entity a)	Return all WasDerivedFrom edges with entity a as an effect.
Collection<WasGeneratedBy>	getWasGeneratedBy()	Return all WasGeneratedBy edges for this graph.
Collection<WasGeneratedBy>	getWasGeneratedBy(Activity p)	Return all WasGeneratedBy edges with activity p as an effect.
Collection<WasGeneratedBy>	getWasGeneratedBy(Entity p)	Return all WasGeneratedBy edges with entity a as a cause.
Collection<WasInformedBy>	getWasInformedBy()	Return all WasInformedBy edges for this graph.
Collection<WasInformedBy>	getWasInformedByWithCause(Activity a)	Return all WasInformedBy edges with activity p as a cause.
Collection<WasInformedBy>	getWasInformedByWithEffect(Activity a)	Return all WasInformedBy edges with activity a as an effect.
IndexedDocument	merge(Document doc)	This function allows a document to be merged with this IndexedDocument.
Document	toDocument()
Set<org.apache.commons.lang3.tuple.Pair<QualifiedName,WasAttributedTo>>	traverseAttributions2(Set<org.apache.commons.lang3.tuple.Pair<QualifiedName,WasAttributedTo>> last, Set<QualifiedName> seen, Stack<QualifiedName> todo)
Set<org.apache.commons.lang3.tuple.Pair<QualifiedName,WasAttributedTo>>	traverseAttributionsWithRelations(QualifiedName from)
Set<QualifiedName>	traverseDerivations(QualifiedName from)
Set<QualifiedName>	traverseDerivations1(Set<QualifiedName> last, Set<QualifiedName> seen, Stack<QualifiedName> todo)
Set<org.apache.commons.lang3.tuple.Pair<QualifiedName,WasDerivedFrom>>	traverseDerivations2(Set<org.apache.commons.lang3.tuple.Pair<QualifiedName,WasDerivedFrom>> last, Set<QualifiedName> seen, Stack<QualifiedName> todo)
Set<org.apache.commons.lang3.tuple.Pair<QualifiedName,WasDerivedFrom>>	traverseDerivationsWithRelations(QualifiedName from)
Set<org.apache.commons.lang3.tuple.Pair<QualifiedName,HadMember>>	traverseMembership2(Set<org.apache.commons.lang3.tuple.Pair<QualifiedName,HadMember>> last, Set<QualifiedName> seen, Stack<QualifiedName> todo)
Set<org.apache.commons.lang3.tuple.Pair<QualifiedName,HadMember>>	traverseMembershipsWithRelations(QualifiedName from)
Set<org.apache.commons.lang3.tuple.Pair<QualifiedName,HadMember>>	traverseReverseMembership2(Set<org.apache.commons.lang3.tuple.Pair<QualifiedName,HadMember>> last, Set<QualifiedName> seen, Stack<QualifiedName> todo)
Set<org.apache.commons.lang3.tuple.Pair<QualifiedName,HadMember>>	traverseReverseMembershipsWithRelations(QualifiedName from)
Set<org.apache.commons.lang3.tuple.Pair<QualifiedName,SpecializationOf>>	traverseSpecializations2(Set<org.apache.commons.lang3.tuple.Pair<QualifiedName,SpecializationOf>> last, Set<QualifiedName> seen, Stack<QualifiedName> todo)
Set<org.apache.commons.lang3.tuple.Pair<QualifiedName,SpecializationOf>>	traverseSpecializationsWithRelations(QualifiedName from)

Methods inherited from class java.lang.Object

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

Constructor Details

IndexedDocument

public IndexedDocument(ProvFactory pFactory,
 Document doc)

IndexedDocument

public IndexedDocument(ProvFactory pFactory,
 Document doc,
 boolean flatten)

Method Details

getUsed

public Collection<Used> getUsed()

Return all used edges for this graph.

Returns:

a collection of Used edges

getUsed

public Collection<Used> getUsed(Activity p)

Return all used edges with activity p as an effect.

Parameters:

p - an activity

Returns:

a collection of Used edges

getUsed

public Collection<Used> getUsed(Entity p)

Return all used edges with entity a as a cause.

Parameters:

p - an entity

Returns:

a collection of Used edges

getWasGeneratedBy

public Collection<WasGeneratedBy> getWasGeneratedBy()

Return all WasGeneratedBy edges for this graph.

Returns:

a collection of WasGeneratedBy edges

getWasGeneratedBy

public Collection<WasGeneratedBy> getWasGeneratedBy(Activity p)

Return all WasGeneratedBy edges with activity p as an effect.

Parameters:

p - an activty

Returns:

a collection of WasGeneratedBy edges

getWasGeneratedBy

public Collection<WasGeneratedBy> getWasGeneratedBy(Entity p)

Return all WasGeneratedBy edges with entity a as a cause.

Parameters:

p - an entity

Returns:

a collection of WasGeneratedBy edges

getWasDerivedFrom

public Collection<WasDerivedFrom> getWasDerivedFrom()

Return all WasDerivedFrom edges for this graph.

Returns:

a collection of WasGeneratedBy edges

getWasDerivedFromWithCause

public Collection<WasDerivedFrom> getWasDerivedFromWithCause(Entity a)

Return all WasDerivedFrom edges with entity a as a cause.

Parameters:

a - an entity

Returns:

a collection of WasDerivedFrom edges

getWasDerivedFromWithEffect

public Collection<WasDerivedFrom> getWasDerivedFromWithEffect(Entity a)

Return all WasDerivedFrom edges with entity a as an effect.

Parameters:

a - an entity

Returns:

a collection of WasDerivedFrom edges

getWasInformedBy

public Collection<WasInformedBy> getWasInformedBy()

Return all WasInformedBy edges for this graph.

Returns:

a collection of WasInformedBy edges

getWasInformedByWithCause

public Collection<WasInformedBy> getWasInformedByWithCause(Activity a)

Return all WasInformedBy edges with activity p as a cause.

Parameters:

a - an activity

Returns:

a collection of WasInformedBy edges

getWasInformedByWithEffect

public Collection<WasInformedBy> getWasInformedByWithEffect(Activity a)

Return all WasInformedBy edges with activity a as an effect.

Parameters:

a - an activity

Returns:

a collection of WasInformedBy edges

getWasAssociatedWith

public Collection<WasAssociatedWith> getWasAssociatedWith()

Return all WasAssociatedWith edges for this graph.

Returns:

a collection of WasAssociatedWith edges

getWasAssociatedWith

public Collection<WasAssociatedWith> getWasAssociatedWith(Activity p)

Return all WasAssociatedWith edges with activity p as an effect.

Parameters:

p - an activity

Returns:

a collection of WasAssociatedWith edges

getWasAssociatedWith

public Collection<WasAssociatedWith> getWasAssociatedWith(Agent a)

Return all WasAssociatedWith edges with entity a as a cause.

Parameters:

a - an agent

Returns:

a collection of WasAssociatedWith edges

add

public Entity add(Entity entity)

add

public Entity add(QualifiedName name,
 Entity entity)

add

public Agent add(Agent agent)

add

public Agent add(QualifiedName name,
 Agent agent)

add

public Activity add(Activity activity)

add

public Activity add(QualifiedName name,
 Activity activity)

getActivity

public Activity getActivity(QualifiedName name)

getEntity

public Entity getEntity(QualifiedName name)

getAgent

public Agent getAgent(QualifiedName name)

add

public WasInformedBy add(WasInformedBy wib)

add

public Used add(Used used)

add

public WasGeneratedBy add(WasGeneratedBy wgb)

add

public WasDerivedFrom add(WasDerivedFrom wdf)

add

public WasAssociatedWith add(WasAssociatedWith waw)

add

public WasAttributedTo add(WasAttributedTo wat)

add

public ActedOnBehalfOf add(ActedOnBehalfOf act)

add

public WasInvalidatedBy add(WasInvalidatedBy wib)

add

public SpecializationOf add(SpecializationOf spec)

add

public AlternateOf add(AlternateOf alt)

add

public WasInfluencedBy add(WasInfluencedBy winf)

add

public WasStartedBy add(WasStartedBy wsb)

add

public WasEndedBy add(WasEndedBy web)

add

public HadMember add(HadMember hm)

add

public <T extends Relation> T add(T statement,
 int num,
 Collection<T> anonRelationCollection,
 HashMap<QualifiedName,Collection<T>> namedRelationMap,
 HashMap<QualifiedName,Collection<T>> effectRelationMap,
 HashMap<QualifiedName,Collection<T>> causeRelationMap)

Add an edge to the graph. Update namedRelationMap, effectRelationMap and causeRelationMap, accordingly. Edges with different attributes are considered distinct.

Type Parameters:

T - the type of the edge to be added

Parameters:

statement - the edge to be added

num - an integer

anonRelationCollection - the collection of anonymous edges

namedRelationMap - the collection of named edges

effectRelationMap - the collection of edges indexed by their effect

causeRelationMap - the collection of edges indexed by their cause

Returns:

the edge that was added

doAction

public void doAction(Activity s)

Specified by:

doAction in interface StatementAction

doAction

public void doAction(Used s)

Specified by:

doAction in interface StatementAction

doAction

public void doAction(WasStartedBy s)

Specified by:

doAction in interface StatementAction

doAction

public void doAction(Agent s)

Specified by:

doAction in interface StatementAction

doAction

public void doAction(AlternateOf s)

Specified by:

doAction in interface StatementAction

doAction

public void doAction(WasAssociatedWith s)

Specified by:

doAction in interface StatementAction

doAction

public void doAction(WasAttributedTo s)

Specified by:

doAction in interface StatementAction

doAction

public void doAction(WasInfluencedBy s)

Specified by:

doAction in interface StatementAction

doAction

public void doAction(ActedOnBehalfOf s)

Specified by:

doAction in interface StatementAction

doAction

public void doAction(WasDerivedFrom s)

Specified by:

doAction in interface StatementAction

doAction

public void doAction(WasEndedBy s)

Specified by:

doAction in interface StatementAction

doAction

public void doAction(Entity s)

Specified by:

doAction in interface StatementAction

doAction

public void doAction(WasGeneratedBy s)

Specified by:

doAction in interface StatementAction

doAction

public void doAction(WasInvalidatedBy s)

Specified by:

doAction in interface StatementAction

doAction

public void doAction(HadMember s)

Specified by:

doAction in interface StatementAction

doAction

public void doAction(MentionOf s)

Specified by:

doAction in interface StatementAction

doAction

public void doAction(SpecializationOf s)

Specified by:

doAction in interface StatementAction

doAction

public void doAction(QualifiedSpecializationOf s)

Specified by:

doAction in interface StatementAction

doAction

public void doAction(QualifiedAlternateOf s)

Specified by:

doAction in interface StatementAction

doAction

public void doAction(QualifiedHadMember s)

Specified by:

doAction in interface StatementAction

doAction

public void doAction(WasInformedBy s)

Specified by:

doAction in interface StatementAction

doAction

public void doAction(DerivedByInsertionFrom s)

Specified by:

doAction in interface StatementAction

doAction

public void doAction(DictionaryMembership s)

Specified by:

doAction in interface StatementAction

doAction

public void doAction(DerivedByRemovalFrom s)

Specified by:

doAction in interface StatementAction

doAction

public void doAction(Bundle bun,
 ProvUtilities provUtilities)

Specified by:

doAction in interface StatementAction

toDocument

public Document toDocument()

merge

public IndexedDocument merge(Document doc)

This function allows a document to be merged with this IndexedDocument. If flatten is true, bundles include in the document will be flattend into this one.

Parameters:

doc - the document to be merged into this

Returns:

this indexed document

traverseDerivations

public Set<QualifiedName> traverseDerivations(QualifiedName from)

traverseDerivations1

public Set<QualifiedName> traverseDerivations1(Set<QualifiedName> last,
 Set<QualifiedName> seen,
 Stack<QualifiedName> todo)

traverseDerivationsWithRelations

public Set<org.apache.commons.lang3.tuple.Pair<QualifiedName,WasDerivedFrom>> traverseDerivationsWithRelations(QualifiedName from)

traverseDerivations2

public Set<org.apache.commons.lang3.tuple.Pair<QualifiedName,WasDerivedFrom>> traverseDerivations2(Set<org.apache.commons.lang3.tuple.Pair<QualifiedName,WasDerivedFrom>> last,
 Set<QualifiedName> seen,
 Stack<QualifiedName> todo)

traverseAttributionsWithRelations

public Set<org.apache.commons.lang3.tuple.Pair<QualifiedName,WasAttributedTo>> traverseAttributionsWithRelations(QualifiedName from)

traverseAttributions2

public Set<org.apache.commons.lang3.tuple.Pair<QualifiedName,WasAttributedTo>> traverseAttributions2(Set<org.apache.commons.lang3.tuple.Pair<QualifiedName,WasAttributedTo>> last,
 Set<QualifiedName> seen,
 Stack<QualifiedName> todo)

traverseMembershipsWithRelations

public Set<org.apache.commons.lang3.tuple.Pair<QualifiedName,HadMember>> traverseMembershipsWithRelations(QualifiedName from)

traverseMembership2

public Set<org.apache.commons.lang3.tuple.Pair<QualifiedName,HadMember>> traverseMembership2(Set<org.apache.commons.lang3.tuple.Pair<QualifiedName,HadMember>> last,
 Set<QualifiedName> seen,
 Stack<QualifiedName> todo)

traverseReverseMembershipsWithRelations

public Set<org.apache.commons.lang3.tuple.Pair<QualifiedName,HadMember>> traverseReverseMembershipsWithRelations(QualifiedName from)

traverseReverseMembership2

public Set<org.apache.commons.lang3.tuple.Pair<QualifiedName,HadMember>> traverseReverseMembership2(Set<org.apache.commons.lang3.tuple.Pair<QualifiedName,HadMember>> last,
 Set<QualifiedName> seen,
 Stack<QualifiedName> todo)

traverseSpecializationsWithRelations

public Set<org.apache.commons.lang3.tuple.Pair<QualifiedName,SpecializationOf>> traverseSpecializationsWithRelations(QualifiedName from)

traverseSpecializations2

public Set<org.apache.commons.lang3.tuple.Pair<QualifiedName,SpecializationOf>> traverseSpecializations2(Set<org.apache.commons.lang3.tuple.Pair<QualifiedName,SpecializationOf>> last,
 Set<QualifiedName> seen,
 Stack<QualifiedName> todo)

getEntities

public Collection<Entity> getEntities()

getActivities

public Collection<Activity> getActivities()

getAgents

public Collection<Agent> getAgents()

checkActivityUsedMap

public void checkActivityUsedMap()

checkEntityWasGeneratedByMap

public void checkEntityWasGeneratedByMap()

checkEntityCauseWasDerivedFromMap

public void checkEntityCauseWasDerivedFromMap()