com.clarkparsia.modularity.AbstractModuleExtractor Maven / Gradle / Ivy
// Copyright (c) 2006 - 2008, Clark & Parsia, LLC.
// This source code is available under the terms of the Affero General Public License v3.
//
// Please see LICENSE.txt for full license terms, including the availability of proprietary exceptions.
// Questions, comments, or requests for clarification: [email protected]
package com.clarkparsia.modularity;
import java.io.IOException;
import java.util.Collection;
import java.util.Collections;
import java.util.EnumSet;
import java.util.HashSet;
import java.util.Set;
import java.util.logging.Level;
import java.util.logging.Logger;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;
import java.util.zip.ZipOutputStream;
import org.mindswap.pellet.PelletOptions;
import org.mindswap.pellet.KnowledgeBase.ChangeType;
import org.mindswap.pellet.taxonomy.Taxonomy;
import org.mindswap.pellet.taxonomy.TaxonomyNode;
import org.mindswap.pellet.utils.MultiValueMap;
import org.mindswap.pellet.utils.Timer;
import org.mindswap.pellet.utils.Timers;
import org.semanticweb.owlapi.model.OWLAxiom;
import org.semanticweb.owlapi.model.OWLClass;
import org.semanticweb.owlapi.model.OWLEntity;
import org.semanticweb.owlapi.model.OWLException;
import org.semanticweb.owlapi.model.OWLOntology;
import com.clarkparsia.modularity.io.ModuleExtractorPersistence;
import com.clarkparsia.modularity.io.UncloseableOutputStream;
import com.clarkparsia.owlapi.modularity.locality.LocalityClass;
import com.clarkparsia.owlapi.modularity.locality.LocalityEvaluator;
import com.clarkparsia.owlapi.modularity.locality.SyntacticLocalityEvaluator;
import com.clarkparsia.owlapiv3.OWL;
import com.clarkparsia.owlapiv3.OntologyUtils;
import com.clarkparsia.pellet.expressivity.Expressivity;
/**
*
* Title:
*
*
* Description:
*
*
* Copyright: Copyright (c) 2007
*
*
* Company: Clark & Parsia, LLC.
*
*
* @author Evren Sirin
*/
public abstract class AbstractModuleExtractor implements ModuleExtractor {
public static final Logger log = Logger
.getLogger( AbstractModuleExtractor.class
.getName() );
private Set additions = new HashSet();
private Set allClasses = new HashSet();
private OWLOntology axiomOntology = null;
/**
* Map to find entities referenced in an axiom
*/
private MultiValueMap axiomEntities = new MultiValueMap();
/**
* Set of axioms that will be deleted
*/
private Set deletions = new HashSet();
/**
* The types of changes that are pending in additions and deletions
*/
protected EnumSet changes = EnumSet.noneOf(ChangeType.class);
/**
* Map to find axioms that references an axiom
*/
protected MultiValueMap entityAxioms = new MultiValueMap();
private LocalityEvaluator localityEvaluator = null;
protected MultiValueMap modules = null;
/**
* Flag to check if a non-local axiom has been updated
*/
private boolean nonLocalAxioms = false;
private Timers timers = new Timers();
public AbstractModuleExtractor() {
this( new SyntacticLocalityEvaluator( LocalityClass.BOTTOM_BOTTOM ) );
}
public AbstractModuleExtractor(LocalityEvaluator localityEvaluator) {
this.localityEvaluator = localityEvaluator;
}
public void addAxiom(OWLAxiom axiom) {
checkNonLocalAxiom( axiom );
if( axiomEntities.containsKey( axiom ) )
return;
if( log.isLoggable( Level.FINE ) )
log.fine( "Adding " + axiom );
deletions.remove( axiom );
additions.add( axiom );
categorizeAddedAxiom( axiom );
}
/**
* Returns if the extracted modules can be updated. We can update the
* modules if we have computed modules and no non-local axiom has been added
* or deleted.
*
* @return
*/
public boolean canUpdate() {
return modules != null && !nonLocalAxioms;
}
/**
* Checks if the given axiom is non-local w.r.t. empty signature and updates
* the {@link #nonLocalAxioms} field.
*
* @param axiom -
* Axiom to be checked
*/
private void checkNonLocalAxiom(OWLAxiom axiom) {
if( !axiom.isLogicalAxiom() )
return;
// no need to check for non-locals if we already know that we cannot
// update modules
if( canUpdate() ) {
if( !isLocal( axiom, Collections.emptySet() ) ) {
log.warning( "*** Non-local axiom: " + axiom );
nonLocalAxioms = true;
}
}
}
public void deleteAxiom(OWLAxiom axiom) {
checkNonLocalAxiom( axiom );
if( !axiomEntities.containsKey( axiom ) ) {
if( additions.remove( axiom ) ) {
if( log.isLoggable( Level.FINE ) )
log.fine( "Deleted axiom from add queue before processing " + axiom );
}
return;
}
if( log.isLoggable( Level.FINE ) )
log.fine( "Deleting " + axiom );
additions.remove( axiom );
deletions.add( axiom );
categorizeRemovedAxiom( axiom );
}
public MultiValueMap getModules() {
return modules;
}
/**
* Extract modules from scratch
*
* @return
*/
public MultiValueMap extractModules() {
Timer timer = timers.startTimer( "extractModules" );
// cache the axiom signatures
processAdditions();
additions.clear();
// no need to consider deletions for initial module extraction
deletions.clear();
changes.clear();
nonLocalAxioms = false;
modules = new MultiValueMap();
extractModuleSignatures( allClasses );
timer.stop();
return modules;
}
/**
* This is a main method to extract the signature for a set of classes Note
* that this method updates the modules for the classes which are maintained
* (either newly created or already existing) in a module partial order
*
* @param entities -
* the set of entities whose modules should be extracted
*/
protected abstract void extractModuleSignatures(Set entities);
/**
* Given an axiom, this function locates all root nodes in the partial order
* that are affected by the update
*
* @param axiom -
* the update
* @param add -
* Flag for additions/deletions
*/
private Set getAffectedRoots(OWLAxiom axiom, Taxonomy taxonomy, boolean add) {
Set roots = new HashSet();
Set> visited = new HashSet>();
visited.add( taxonomy.getBottom() );
getAffectedRoots( axiom, taxonomy.getTop(), roots, add, visited );
/*
* Special case when the only node affected by a deletion is
* unsatisfiable
*/
if( !add && roots.isEmpty() ) {
for( OWLClass unsat : taxonomy.getEquivalents( OWL.Nothing ) ) {
Set signature = modules.get( unsat );
if( (signature != null) && signature.containsAll( getSignature( axiom ) ) )
roots.add( unsat );
}
}
return roots;
}
/**
* Given an axiom, this function locates all root nodes in the partial order
* that are affected by the update
*
* @param axiom -
* the update
* @param node -
* the next node
* @param effects -
* the actual set of affected nodes collected
* @param add -
* Flag for additions/deletions
* @param visited -
* nodes visited so far
*/
private void getAffectedRoots(OWLAxiom axiom, TaxonomyNode node,
Set effects, boolean add, Set> visited) {
// only proceed if not seen this node
if( visited.contains( node ) )
return;
else
visited.add( node );
OWLEntity entity = node.getName();
// get the sig for this module
Set signature = modules.get( entity );
boolean outdated = false;
// check if the entity has been removed due to a deletion
if( signature == null ) {
if( log.isLoggable( Level.FINE ) )
log.fine( "Removed entity " + entity );
}
else if( add ) {
// only affected if axiom is non-local w.r.t. the sig of the
// module
outdated = !isLocal( axiom, signature );
}
else {
// only affected if sig of axiom is contained in sig of module
outdated = signature.containsAll( getSignature( axiom ) );
}
// if outdated add to effected set
if( outdated ) {
effects.addAll( node.getEquivalents() );
}
else {
// recursive call to children
for( TaxonomyNode next : node.getSubs() ) {
getAffectedRoots( axiom, next, effects, add, visited );
}
}
}
/**
* Return the axioms which references this entity
*
* @param entity
* @return
*/
public Set getAxioms(OWLEntity entity) {
Set axioms = entityAxioms.get( entity );
if( axioms == null )
axioms = Collections.emptySet();
return axioms;
}
public OWLOntology getModule(OWLEntity entity) {
return getModuleFromSignature( modules.get( entity ) );
}
protected Set getModuleAxioms(Set signature) {
Set referenced = new HashSet();
Set augmentedSig = new HashSet( signature );
augmentedSig.add( OWL.Thing );
Set axioms = new HashSet();
Set candidates = new HashSet();
for( OWLEntity e : signature ) {
candidates.addAll( getAxioms( e ) );
}
for( OWLAxiom axiom : candidates ) {
Set sigAxiom = axiomEntities.get( axiom );
/*
* An axiom is in the module of the signature if the augmented
* signature contains all the entities referenced in the axiom.
* However, there are cases this necessary condition is not
* sufficient. For example, an axiom may be a tautology, e.g.
* PropertyDomain(p owl:Thing), and if this axiom is included the
* module would not be minimal anymore. The locality check we
* perform for the axiom w.r.t. the given signature filters these
* axioms.
*/
if( augmentedSig.containsAll( sigAxiom ) && !isLocal( axiom, signature ) ) {
axioms.add( axiom );
referenced.addAll( sigAxiom );
}
}
/*
* Special handling is required if an entity is in the input signature,
* and is referenced by some axioms, but all those axioms are local to
* the signature and contain entities not in the signature. A
* declaration axiom is used to keep the entity in the module.
*/
Set notReferenced = new HashSet( signature );
notReferenced.removeAll( referenced );
for( OWLEntity e : notReferenced ) {
if( entityAxioms.get( e ) != null )
axioms.add( OWL.declaration( e ) );
}
return axioms;
}
/**
* Returns a new ontology that contains the axioms that are in the module
* for given set of entities
*
* @param signature
* @return
* @throws OWLException
*/
public OWLOntology getModuleFromSignature(Set signature) {
Set moduleAxioms = getModuleAxioms( signature );
return OWL.Ontology( moduleAxioms );
}
/**
* Get the entities referenced in this axiom
*
* @param axiom
* @return
*/
protected Set getSignature(OWLAxiom axiom) {
return axiomEntities.get( axiom );
}
/**
* Checks if axioms have been added/removed and modules need to be updated
*
* @return true if axioms have been added/removed
*/
public boolean isChanged() {
return !additions.isEmpty() || !deletions.isEmpty() || nonLocalAxioms;
}
protected boolean isLocal(OWLAxiom axiom, Set signature) {
return localityEvaluator.isLocal( axiom, signature );
}
public void addOntologies(Set ontologies) {
for( OWLOntology ontology : ontologies )
addOntology( ontology );
}
public void addOntology(OWLOntology ontology) {
for( OWLAxiom axiom : ontology.getAxioms() )
addAxiom( axiom );
}
private void processAdditions() {
for( OWLAxiom axiom : additions ) {
Set signature = OntologyUtils.getSignature( axiom );
axiomEntities.put( axiom, signature );
for( OWLEntity entity : signature ) {
entityAxioms.add( entity, axiom );
if( entity instanceof OWLClass ) {
OWLClass cls = (OWLClass) entity;
allClasses.add( cls );
}
}
}
}
private void processDeletions() {
for( OWLAxiom axiom : deletions ) {
Set entities = axiomEntities.remove( axiom );
for( OWLEntity entity : entities ) {
entityAxioms.remove( entity, axiom );
if( !entityAxioms.containsKey( entity ) ) {
if( log.isLoggable( Level.FINE ) )
log.fine( "Remove " + entity + " which is not mentioned anymore" );
allClasses.remove( entity );
modules.remove( entity );
}
}
}
}
/**
* Method to 1) find affected modules and 2) update them - that is extract
* their new signatures
*
* @param Map
* axiomMap Index from the new/deleted axioms to their signature
* @param Segmentation
* seg handle on segmentation for this ontology
* @param boolean
* add Flag for additions/deletions
*/
private Set updateEffectedModules(Set axioms, Taxonomy taxonomy,
boolean add) {
// affected root nodes in order
Set affectedRoots = new HashSet();
// Set of all nodes affected
Set affected = new HashSet();
// Set of all entities in the module of affected entities
Set effects = new HashSet();
if( log.isLoggable( Level.FINE ) )
log.fine( "Update modules for " + (add
? "additions"
: "deletions") );
// any new classes are affected
affectedRoots.addAll( allClasses );
affectedRoots.removeAll( modules.keySet() );
// iterate over all axioms and get find the set of root nodes
// affected by the update
for( OWLAxiom axiom : axioms ) {
// find affected roots - recursive function
affectedRoots.addAll( getAffectedRoots( axiom, taxonomy, add ) );
}
if( log.isLoggable( Level.FINE ) )
log.fine( "Affected roots " + affectedRoots );
// given root, get all affected objects
for( OWLEntity nextRoot : affectedRoots ) {
// add root to affected
affected.add( nextRoot );
if( nextRoot instanceof OWLClass ) {
// collect all the descendants of this class
if( taxonomy.contains( (OWLClass) nextRoot ) )
affected.addAll( taxonomy.getFlattenedSubs( (OWLClass) nextRoot, false ) );
}
}
if( log.isLoggable( Level.FINE ) )
log.fine( "Affected entities " + affected );
for( OWLEntity entity : affected )
modules.remove( entity );
// Next update mods of all affected nodes
extractModuleSignatures( affected );
for( OWLEntity entity : affected ) {
Set module = modules.get( entity );
if( module == null ) {
String msg = "No module for " + entity;
log.log( Level.SEVERE, msg, new RuntimeException( msg ) );
}
effects.addAll( module );
}
return effects;
}
/**
* Update the modules with the changes that have been put into the queue so
* far.
*
* @param add
* If true apply only addition changes, otherwise
* apply deletions
* @return The set of entities whose modules are affected by the changes
* @throws UnsupportedOperationException
* if modules cannot be updated as reported by
* {@link #canUpdate()} function
*/
public Set updateModules(Taxonomy taxonomy, boolean add)
throws UnsupportedOperationException {
Timer timer = timers.startTimer( "updateModules" );
if( !canUpdate() )
throw new UnsupportedOperationException( "Modules cannot be updated!" );
Set effects = null;
if( add ) {
// cash the signatures for axioms as they are used in the next step
processAdditions();
// compute effects
effects = updateEffectedModules( additions, taxonomy, add );
// clear processed axioms
additions.clear();
// update the pending change types -- remove the changes
// that are additions
changes.remove(ChangeType.ABOX_ADD);
changes.remove(ChangeType.RBOX_ADD);
changes.remove(ChangeType.TBOX_ADD);
}
else {
// compute effects
effects = updateEffectedModules( deletions, taxonomy, add );
// remove signatures for deleted axioms now that they are not needed
processDeletions();
// clear processed axioms
deletions.clear();
// update the pending change types -- remove the changes
// that are additions
changes.remove(ChangeType.ABOX_DEL);
changes.remove(ChangeType.RBOX_DEL);
changes.remove(ChangeType.TBOX_DEL);
}
timer.stop();
return effects;
}
public Timers getTimers() {
return timers;
}
public Set getAxioms() {
return Collections.unmodifiableSet( axiomEntities.keySet() );
}
public OWLOntology getAxiomOntology() {
if ( null == axiomOntology ) {
axiomOntology = OWL.Ontology( axiomEntities.keySet() );
}
return axiomOntology;
}
public Set getEntities() {
return Collections.unmodifiableSet( entityAxioms.keySet() );
}
public void resetModules() {
// cache the axiom signatures
processAdditions();
additions.clear();
// no need to consider deletions for initial module extraction
deletions.clear();
changes.clear();
nonLocalAxioms = false;
modules = new MultiValueMap();
}
/**
* @inheritDoc
*/
public boolean isClassificationNeeded(Expressivity expressivity) {
return
isTBoxChanged()
// RBox did not change since classification
|| isRBoxChanged()
// there are no nominals
|| (expressivity.hasNominal() && !PelletOptions.USE_PSEUDO_NOMINALS);
}
/**
* Checks whether there are unapplied changes to the TBox
*
* @return true if there are unapplied changes to TBox
*/
public boolean isTBoxChanged() {
return changes.contains( ChangeType.TBOX_ADD ) || changes.contains( ChangeType.TBOX_DEL );
}
/**
* Checks whether there are unapplied changes to the RBox
*
* @return true if there are unapplied changes to RBox
*/
public boolean isRBoxChanged() {
return changes.contains( ChangeType.RBOX_ADD ) || changes.contains( ChangeType.RBOX_DEL );
}
/**
* Checks whether there are unapplied changes to the ABox
*
* @return true if there are unapplied changes to ABox
*/
public boolean isABoxChanged() {
return changes.contains( ChangeType.ABOX_ADD ) || changes.contains( ChangeType.ABOX_DEL );
}
/**
* Checks the category of the change the addition of the axiom introduces
* (i.e., change to a TBox, RBox, or ABox), and updates the changes set appropriately.
*
* @param axiom the axiom being added
*/
private void categorizeAddedAxiom(OWLAxiom axiom) {
if (ChangeTypeDetector.isTBoxAxiom(axiom)) {
changes.add(ChangeType.TBOX_ADD);
}
else if (ChangeTypeDetector.isRBoxAxiom(axiom)) {
changes.add(ChangeType.RBOX_ADD);
}
else if (ChangeTypeDetector.isABoxAxiom(axiom)) {
changes.add(ChangeType.ABOX_ADD);
}
}
/**
* Checks the category of the change the deletion of the axiom introduces
* (i.e., change to a TBox, RBox, or ABox), and updates the changes set appropriately.
*
* @param axiom the axiom being removed
*/
private void categorizeRemovedAxiom(OWLAxiom axiom) {
if (ChangeTypeDetector.isTBoxAxiom(axiom)) {
changes.add(ChangeType.TBOX_DEL);
}
else if (ChangeTypeDetector.isRBoxAxiom(axiom)) {
changes.add(ChangeType.RBOX_DEL);
}
else if (ChangeTypeDetector.isABoxAxiom(axiom)) {
changes.add(ChangeType.ABOX_DEL);
}
}
// I/O code to persist the state of the AbstractModuleExtractor
/**
* The name of the entry in the zip file that stores axioms
*/
private static final String MODULE_EXTRACTOR_AXIOMS_FILE_NAME = "ModuleExtractorAxioms";
/**
* The name of the entry in the zip file that stores the module information
*/
private static final String MODULE_EXTRACTOR_MODULES_FILE_NAME = "ModuleExtractorModules";
/**
* @inheritDoc
*/
public void save(ZipOutputStream outputStream) throws IOException, IllegalStateException {
if ( !additions.isEmpty() || !deletions.isEmpty() ) {
throw new IllegalStateException( "The module extractor contains unapplied changes to the modules, and therefore cannot be saved." );
}
// first save the axioms
ZipEntry axiomsEntry = new ZipEntry( MODULE_EXTRACTOR_AXIOMS_FILE_NAME );
outputStream.putNextEntry( axiomsEntry );
ModuleExtractorPersistence.saveAxioms( axiomEntities.keySet(), new UncloseableOutputStream( outputStream ) );
// next save the modules
ZipEntry modulesEntry = new ZipEntry( MODULE_EXTRACTOR_MODULES_FILE_NAME );
outputStream.putNextEntry( modulesEntry );
ModuleExtractorPersistence.saveModules( modules, new UncloseableOutputStream( outputStream ) );
outputStream.flush();
}
/**
* @inheritDoc
*/
public void load(ZipInputStream inputStream) throws IOException, IllegalArgumentException {
resetModules();
ZipEntry zipEntry = inputStream.getNextEntry();
if( !( MODULE_EXTRACTOR_AXIOMS_FILE_NAME.equals( zipEntry.getName() ) ) ) {
throw new IllegalArgumentException( String.format( "Unexpected entry (%s) in ZipInputStream. Expected %s", zipEntry.getName(), MODULE_EXTRACTOR_AXIOMS_FILE_NAME ) );
}
axiomOntology = ModuleExtractorPersistence.loadAxiomOntology( inputStream );
Collection axioms = axiomOntology.getAxioms();
// I am not sure that this is the right way to recompute this ...
additions.addAll( axioms );
processAdditions();
additions.clear();
zipEntry = inputStream.getNextEntry();
if( !( MODULE_EXTRACTOR_MODULES_FILE_NAME.equals( zipEntry.getName() ) ) ) {
throw new IllegalArgumentException( String.format( "Unexpected entry (%s) in ZipInputStream. Expected %s", zipEntry.getName(), MODULE_EXTRACTOR_MODULES_FILE_NAME ) );
}
modules = ModuleExtractorPersistence.loadModules( inputStream );
}
}