/**
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
* distributed with this work for additional information
* regarding copyright ownership. The ASF licenses this file
* to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
* with the License. You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.apache.marmotta.kiwi.reasoner.engine;
import com.google.common.base.Equivalence;
import com.google.common.collect.HashMultimap;
import com.google.common.collect.Multimap;
import info.aduna.iteration.CloseableIteration;
import info.aduna.iteration.EmptyIteration;
import info.aduna.iteration.Iterations;
import info.aduna.iteration.SingletonIteration;
import org.apache.marmotta.commons.sesame.model.StatementCommons;
import org.apache.marmotta.kiwi.model.caching.TripleTable;
import org.apache.marmotta.kiwi.model.rdf.KiWiNode;
import org.apache.marmotta.kiwi.model.rdf.KiWiResource;
import org.apache.marmotta.kiwi.model.rdf.KiWiTriple;
import org.apache.marmotta.kiwi.model.rdf.KiWiUriResource;
import org.apache.marmotta.kiwi.reasoner.model.exception.ReasoningException;
import org.apache.marmotta.kiwi.reasoner.model.exception.UnjustifiedTripleException;
import org.apache.marmotta.kiwi.reasoner.model.program.*;
import org.apache.marmotta.kiwi.reasoner.model.query.QueryResult;
import org.apache.marmotta.kiwi.reasoner.persistence.KiWiReasoningConnection;
import org.apache.marmotta.kiwi.reasoner.persistence.KiWiReasoningPersistence;
import org.apache.marmotta.kiwi.sail.KiWiSailConnection;
import org.apache.marmotta.kiwi.transactions.api.TransactionListener;
import org.apache.marmotta.kiwi.transactions.api.TransactionalSail;
import org.apache.marmotta.kiwi.transactions.model.TransactionData;
import org.openrdf.model.Resource;
import org.openrdf.model.Statement;
import org.openrdf.model.URI;
import org.openrdf.model.Value;
import org.openrdf.sail.SailConnection;
import org.openrdf.sail.SailException;
import org.openrdf.sail.helpers.SailConnectionWrapper;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.sql.SQLException;
import java.util.*;
import java.util.concurrent.LinkedBlockingQueue;
import java.util.concurrent.locks.Lock;
import java.util.concurrent.locks.ReentrantLock;
/**
* This class implements the evaluation of reasoning programs on the triple store. It has two different modes:
* <ul>
* <li>incremental reasoning: when new triples are added or old triples are removed, the inferred information is updated accordingly</li>
* <li>full reasoning: (re-)runs the reasoning process over all triples currently contained in the triple store</li>
* </ul>
* Since reasoning can require some time, the actual execution of incremental reasonong is implemented in a
* producer-consumer style. When new transaction data is available, it is added to a queue. A separate reasoning
* thread then takes new transaction data and processes the rules asynchronously.
* <p/>
* The reasoning engine uses its own connection to the database to carry out reasoning tasks.
* <p/>
* TODO: we need to clarify conceptually whether it would be correct to run several reasoner threads in parallel.
* In theory, reasoning here is strictly monotonic so there should not be a problem. In practice, we might miss
* certain triples because the order of transactions might be messed up. Maybe it makes more sense to parallelize
* the execution or rules instead.
* <p/>
* User: Sebastian Schaffert (sschaffert@apache.org)
*/
public class ReasoningEngine implements TransactionListener {
private static Logger log = LoggerFactory.getLogger(ReasoningEngine.class);
private static final String TASK_GROUP = "Reasoner";
/**
* A queue of transaction data objects of committed transactions, will be consumed by the reasoner
* thread in incremental reasoning.
*/
private LinkedBlockingQueue<TransactionData> reasoningQueue;
/**
* A direct connection to the database to perform queries and store program-related information
*/
private KiWiReasoningPersistence persistence;
/**
* A connection to the underlying KiWiStore to store new inferred triples and to access the value
* factory.
*/
private TransactionalSail store;
/**
* Configuration for this reasoning engine.
*/
private ReasoningConfiguration config;
/**
* In-memory cache of the currently active reasoning programs, (re-)initialized by {@link #loadPrograms()}.
*/
private List<Program> programs;
/**
* In-memory cache to store all patterns that are candidates for matching triples and accessing the rules
* they belong to.
*/
private Multimap<Pattern,Rule> patternRuleMap;
/**
* Internal counter to count executions of the reasoner (informational purposes only)
*/
private static long taskCounter = 0;
private boolean isshutdown = false;
/**
* The worker thread for the reasoner.
*/
private SKWRLReasoner reasonerThread;
protected static Equivalence<Statement> equivalence = StatementCommons.quadrupleEquivalence();
/**
* A lock to ensure that only once thread at a time is carrying out persistence
*/
private Lock persistenceLock;
// for mocking
protected ReasoningEngine() {
}
public ReasoningEngine(KiWiReasoningPersistence persistence, TransactionalSail store, ReasoningConfiguration config) {
this.persistence = persistence;
this.store = store;
this.config = config;
this.persistenceLock = new ReentrantLock();
loadPrograms();
this.reasoningQueue = new LinkedBlockingQueue<TransactionData>();
this.reasonerThread = new SKWRLReasoner();
}
public void loadPrograms() {
log.info("program configuration changed, reloading ...");
patternRuleMap = HashMultimap.<Pattern,Rule>create();
try {
KiWiReasoningConnection connection = persistence.getConnection();
try {
programs = Iterations.asList(connection.listPrograms());
for(Program p : programs) {
for(Rule rule : p.getRules()) {
for(Pattern pattern : rule.getBody()) {
patternRuleMap.put(pattern,rule);
}
}
}
} finally {
connection.close();
}
} catch (SQLException ex) {
programs = Collections.emptyList();
log.warn("cannot load reasoning programs, reasoning disabled (error message: {})", ex.getMessage());
}
}
public void programChanged(Program program) {
}
/**
* In case a new rule has been added to one of the reasoning programs, process only this rule addition
* incrementally. Since the reasoner is strictly monotonic, this is sufficient.
*
* @param rule
*/
public void notifyAddRule(Rule rule) {
startTask("Addition of rule " + rule.getName(), TASK_GROUP);
log.debug("processing new rule: {}", rule);
try {
updateTaskStatus("processing new rule ...");
processRule(rule, null, null);
} catch(Exception ex) {
log.error("error while processing rule",ex);
return;
} finally {
endTask();
}
}
/**
* In case an existing rule has been removed from one of the reasoning programs, remove all triples
* that are based on this rule by consulting the justifications that use this rule. Since the reasoner
* is strictly monotonic, this is sufficient to get the correct set of materialized triples.
*
*/
public void notifyRemoveRules() {
startTask("Removing Rules", TASK_GROUP);
// clean up justifications depending on the rule
updateTaskStatus("cleaning up unsupported triples");
try {
KiWiReasoningConnection connection = persistence.getConnection();
try {
// this is done automatically now when updating or deleting a program:
// removeJustificationsByQuery("reasoner.listJustificationsByRule", ImmutableMap.of("rule", (Object) rule));
// then remove all inferred triples that are no longer supported
cleanupUnsupported(connection);
// and finally garbage collect those triples that are inferred and deleted
// garbage collection is now carried out by a thread in the triple store
//garbageCollectTriples();
} catch (SQLException ex) {
connection.rollback();
throw ex;
} finally {
connection.close();
}
} catch (SailException ex) {
log.error("REPOSITORY ERROR: could not clean up unsupported triples, database state will be inconsistent! Message: {}", ex.getMessage());
log.debug("Exception details:", ex);
} catch (SQLException ex) {
log.error("DATABASE ERROR: could not clean up justifications for triples, database state will be inconsistent! Message: {}", ex.getMessage());
log.debug("Exception details:", ex);
}
endTask();
}
/**
* Incrementally apply the updates that are contained in the transaction
* data to the reasoning programs that are in the system.
* <p/>
* Called after a transaction has committed. The transaction data will contain all changes done in the transaction since
* the last commit. This method should be used in case the transaction listener aims to perform additional activities
* in a new transaction or outside the transaction management, e.g. notifying a server on the network, adding
* data to a cache, or similar.
*
* @param data
*/
@Override
public void afterCommit(TransactionData data) {
if( (data.getAddedTriples().size() > 0 || data.getRemovedTriples().size() > 0) && patternRuleMap.size() > 0) {
reasoningQueue.remove(data);
if (!reasoningQueue.offer(data)) {
log.info("waiting for reasoning queue to become available ...");
try {
reasoningQueue.put(data);
log.info("reasoning queue available, added data");
} catch (InterruptedException e) {
log.error("interrupted while waiting for reasoning queue to become available ...");
}
};
}
}
/**
* Called before a transaction commits. The transaction data will contain all changes done in the transaction since
* the last commit. This method should be used in case the transaction listener aims to perform additional activities
* in the same transaction, like inserting or updating database tables.
*
* @param data
*/
@Override
public void beforeCommit(TransactionData data) {
// do nothing
}
/**
* Called when a transaction rolls back.
*/
@Override
public void rollback(TransactionData data) {
// do nothing
}
/**
* Start a new reasoner task to collect status messages. Informational purposes only.
* @param name
*/
protected void startTask(String name, String taskGroup) {
// if a task is already running, this should create a nested subtask
}
/**
* Stop the currently active reasoning task. Informational purposes only.
*/
protected void endTask() {
}
/**
* Update the status of the reasoner task with the given message. This will simply send all update messages to
* registered status listeners.
* @param message
*/
protected void updateTaskStatus(String message) {
}
/**
* Update the task progress (if any)
* @param progress
*/
protected void updateTaskProgress(int progress) {
}
/**
* Set the maximum steps needed in the task progress (if any)
* @param progress
*/
protected void updateTaskMaxProgress(int progress) {
}
private void executeReasoner(TransactionData data) {
try {
updateTaskStatus("fetching worklist");
Set<KiWiTriple> newTriples = StatementCommons.newQuadrupleSet();
for(Statement stmt : data.getAddedTriples()) {
KiWiTriple t = (KiWiTriple)stmt;
if(t.isMarkedForReasoning()) {
newTriples.add(t);
t.setMarkedForReasoning(false);
}
}
//taskManagerService.setTaskSteps(newTriples.size() + data.getRemovedTriples().size());
// evaluate the rules for all added triples
if(newTriples.size() > 0) {
long start2 = System.currentTimeMillis();
updateTaskStatus("reasoning over " + newTriples.size() + " new triples");
processRules(newTriples);
log.debug("REASONER: reasoning for {} new triples took {} ms overall", newTriples.size(), System.currentTimeMillis() - start2);
}
if(data.getRemovedTriples().size() > 0) {
log.debug("cleaning up justifications and inferences for {} triples",data.getRemovedTriples().size());
try {
KiWiReasoningConnection connection = persistence.getConnection();
try {
// first clean up justifications that are no longer supported
cleanupJustifications(connection, data.getRemovedTriples());
// then remove all inferred triples that are no longer supported
cleanupUnsupported(connection);
// and finally garbage collect those triples that are inferred and deleted
// garbage collection is now carried out by a thread in the triple store
//garbageCollectTriples();
connection.commit();
} catch (SQLException ex) {
connection.rollback();
throw ex;
} finally {
connection.close();
}
} catch (SailException | SQLException ex) {
log.error("REASONING ERROR: could not clean up unsupported triples, database state will be inconsistent! Message: {}", ex.getMessage());
log.debug("Exception details:", ex);
throw ex;
}
}
} catch (SQLException | SailException | ReasoningException ex) {
log.error("REASONER: processing of transaction data with ID {} aborted; reason: {}", data.getTransactionId(), ex.getMessage());
}
}
/**
* Clean all inferred triples and re-run all reasoning rules.
*/
public void reRunPrograms() {
final String taskName = "Reasoner Task "+ ++taskCounter + " (full reasoning)";
startTask("Synchronous " + taskName, TASK_GROUP);
executeReasoner();
endTask();
}
/**
* Perform a full reasoning over the triples and rules contained in the database. Will first remove all existing
* inferred triples and justifications and then evaluate each of the rules in turn.
*/
private void executeReasoner() {
// clean up all justifications
updateTaskStatus("removing old justifications");
try {
KiWiReasoningConnection connection = persistence.getConnection();
try {
// remove all justifications from the database
connection.deleteJustifications();
// clean up inferred triples by removing them from the triple store; the transaction system should take care of the rest
cleanupUnsupported(connection);
// and finally garbage collect those triples that are inferred and deleted
// garbage collection is now carried out by a thread in the triple store
//garbageCollectTriples();
connection.commit();
} catch (SQLException ex) {
connection.rollback();
throw ex;
} finally {
connection.close();
}
} catch (SailException ex) {
log.error("REPOSITORY ERROR: could not clean up unsupported triples, database state will be inconsistent! Message: {}", ex.getMessage());
log.debug("Exception details:", ex);
} catch (SQLException ex) {
log.error("DATABASE ERROR: could not clean up justifications for triples, database state will be inconsistent! Message: {}", ex.getMessage());
log.debug("Exception details:", ex);
}
// process the rules over the whole dataset
try {
updateTaskStatus("processing rules ...");
//Set<Callable<Boolean>> tasks = new HashSet<Callable<Boolean>>();
for(Program p : programs) {
for(final Rule rule : p.getRules()) {
startTask("Rule Processing", TASK_GROUP);
updateTaskStatus("processing rule " + rule.getName() + " ...");
processRule(rule, null, null);
endTask();
// TODO: multithreading is currently not working reliably (some nodes might get inserted twice)
/*
tasks.add(new Callable<Boolean>() {
@Override
public Boolean call() throws Exception {
startTask("Rule Processing", TASK_GROUP);
updateTaskStatus("processing rule " + rule.getName() + " ...");
processRule(rule, null, null);
endTask();
return Boolean.TRUE;
}
});
*/
}
}
//workers.invokeAll(tasks);
} catch(Exception ex) {
log.error("error while processing rules", ex);
return;
}
}
/**
* This method iterates over all triples that are passed as argument and
* checks whether they are used as supporting triples justifications. All
* such justifications are removed. Triples that are no longer supported
* will later be cleaned up by {@link #cleanupUnsupported(org.apache.marmotta.kiwi.reasoner.persistence.KiWiReasoningConnection)}
*
* @param removedTriples
*/
private void cleanupJustifications(KiWiReasoningConnection connection, TripleTable<Statement> removedTriples) throws SQLException {
updateTaskStatus("cleaning up justifications for " + removedTriples.size() + " removed triples");
for(Statement stmt : removedTriples) {
KiWiTriple t = (KiWiTriple)stmt;
connection.deleteJustifications(t);
}
}
/**
* Cleanup inferred triples that are no longer supported by any justification.
*/
private void cleanupUnsupported(KiWiReasoningConnection connection) throws SQLException, SailException {
updateTaskStatus("cleaning up unsupported triples");
int count = 0, total = 0;
startTask("Unsupported Triple Cleaner", TASK_GROUP);
updateTaskStatus("loading unsupported triples");
CloseableIteration<KiWiTriple,SQLException> tripleIterator = connection.listUnsupportedTriples();
try {
if(tripleIterator.hasNext()) {
updateTaskStatus("deleting unsupported triples");
SailConnection tc = store.getConnection();
KiWiSailConnection ic = getWrappedConnection(tc);
try {
tc.begin();
while(tripleIterator.hasNext()) {
ic.removeInferredStatement(tripleIterator.next());
count++;
}
log.debug("removed {} unsupported triples",count);
tc.commit();
} catch(SailException ex) {
ic.rollback();
throw ex;
} finally {
ic.close();
}
}
} finally {
Iterations.closeCloseable(tripleIterator);
}
}
/**
*
* @param addedTriples
*/
private void processRules(final Set<KiWiTriple> addedTriples) throws SQLException, SailException, ReasoningException {
updateTaskStatus("processing rules ...");
// select the rules that have at least one matching pattern; the match method will
// return a set of variable bindings that we will be used to prepopulate the bindings
for(final Pattern pattern : patternRuleMap.keySet()) {
for(KiWiTriple triple : addedTriples) {
QueryResult match = matches(pattern,triple);
if(match != null) {
for(Rule rule : patternRuleMap.get(pattern)) {
log.debug("REASONER(rule '{}'): pattern {} matched with triple {}", rule.getName(), pattern.toString(), triple.toString());
processRule(rule, match, pattern);
}
}
}
}
}
/**
* Process the rule given as argument. The set of bindings passed as argument is used as a seed of
* bindings and will be further populated by pattern matches. The set of justifications is passed over
* from previous calls so that justifications can be persisted in a batch.
*
* @param rule
* @param match
*/
private void processRule(Rule rule, QueryResult match, Pattern p) throws SQLException, SailException, ReasoningException {
// get the variable bindings for the rule evaluation
log.debug("REASONER(rule '{}'): evaluating rule body {} ...", rule.getName() != null ? rule.getName() : rule.getId(), rule);
// create a collection consisting of the body minus the pattern that already matched
Set<Pattern> body = new HashSet<Pattern>(rule.getBody());
if(p != null) {
body.remove(p);
}
CloseableIteration<QueryResult, SQLException> bodyResult;
KiWiReasoningConnection connection = persistence.getConnection();
SailConnection sail = store.getConnection();
KiWiSailConnection isail = getWrappedConnection(sail);
try {
// if there are further patterns, evaluate them; if the matched pattern was the only pattern, then
// simply take the match as binding
if(body.size() > 0) {
bodyResult = connection.query(body,match,null,null,true);
} else if(match != null) {
bodyResult = new SingletonIteration<QueryResult, SQLException>(match);
} else {
bodyResult = new EmptyIteration<QueryResult, SQLException>();
}
// construct triples out of the bindings and the rule heads
long counter = 0;
// initialise a new set of justifications
Set<Justification> justifications = new HashSet<Justification>();
sail.begin();
while(bodyResult.hasNext()) {
QueryResult row = bodyResult.next();
Map<VariableField,KiWiNode> binding = row.getBindings();
Resource subject = null;
URI property = null;
Value object;
if(rule.getHead().getSubject() != null && rule.getHead().getSubject().isVariableField()) {
if(!binding.get(rule.getHead().getSubject()).isUriResource() && !binding.get(rule.getHead().getSubject()).isAnonymousResource()) {
log.info("cannot use value {} as subject, because it is not a resource",binding.get(rule.getHead().getSubject()));
continue;
}
subject = (KiWiResource)binding.get(rule.getHead().getSubject());
} else if(rule.getHead().getSubject() != null && rule.getHead().getSubject().isResourceField()) {
subject = ((ResourceField)rule.getHead().getSubject()).getResource();
} else
throw new IllegalArgumentException("Subject of rule head may only be a variable or a resource; rule: "+rule);
if(rule.getHead().getProperty() != null && rule.getHead().getProperty().isVariableField()) {
if(!binding.get(rule.getHead().getProperty()).isUriResource()) {
log.info("cannot use value {} as property, because it is not a URI resource",binding.get(rule.getHead().getProperty()));
continue;
}
property = (KiWiUriResource)binding.get(rule.getHead().getProperty());
} else if(rule.getHead().getProperty() != null && rule.getHead().getProperty().isResourceField()) {
property = (KiWiUriResource)((ResourceField)rule.getHead().getProperty()).getResource();
} else
throw new IllegalArgumentException("Property of rule head may only be a variable or a resource; rule: "+rule);
if(rule.getHead().getObject() != null && rule.getHead().getObject().isVariableField()) {
object = binding.get(rule.getHead().getObject());
} else if(rule.getHead().getObject() != null && rule.getHead().getObject().isResourceField()) {
object = ((ResourceField)rule.getHead().getObject()).getResource();
} else if(rule.getHead().getObject() != null && rule.getHead().getObject().isLiteralField()) {
object = ((LiteralField)rule.getHead().getObject()).getLiteral();
} else
throw new IllegalArgumentException("Object of rule head may only be a variable, a literal, or a resource; rule: "+rule);
KiWiTriple triple = isail.addInferredStatement(subject, property, object);
Justification justification = new Justification();
justification.setTriple(triple);
justification.getSupportingRules().add(rule);
justification.getSupportingTriples().addAll(row.getJustifications());
justifications.add(justification);
// when the batch size is reached, commit the transaction, save the justifications, and start a new
// transaction and new justification set
if(++counter % config.getBatchSize() == 0) {
persistenceLock.lock();
try {
sail.commit();
log.debug("adding {} justifications",justifications.size());
updateTaskStatus("storing justifications ...");
Set<Justification> baseJustifications = getBaseJustifications(connection,justifications);
if(config.isRemoveDuplicateJustifications()) {
removeDuplicateJustifications(connection,baseJustifications);
}
log.debug("{} justifications added after resolving inferred triples", baseJustifications.size());
// persist the justifications that have been created in the rule processing
if(baseJustifications.size() > 0) {
connection.storeJustifications(baseJustifications);
}
connection.commit();
sail.begin();
} finally {
persistenceLock.unlock();
}
justifications.clear();
}
}
persistenceLock.lock();
try {
sail.commit();
log.debug("adding {} justifications",justifications.size());
updateTaskStatus("storing justifications ...");
Set<Justification> baseJustifications = getBaseJustifications(connection,justifications);
if(config.isRemoveDuplicateJustifications()) {
removeDuplicateJustifications(connection,baseJustifications);
}
// persist the justifications that have been created in the rule processing
if(baseJustifications.size() > 0) {
connection.storeJustifications(baseJustifications);
}
log.debug("{} justifications added after resolving inferred triples", baseJustifications.size());
Iterations.closeCloseable(bodyResult);
connection.commit();
} finally {
persistenceLock.unlock();
}
} catch(SailException | SQLException | ReasoningException ex) {
log.error("REASONING ERROR: could not process rule, database state will be inconsistent! Message: {}",ex.getMessage());
log.debug("Exception details:",ex);
connection.rollback();
sail.rollback();
throw ex;
} finally {
connection.close();
sail.close();
}
}
/**
* Return the justifications for the triple passed as argument.
* @param t
* @return
*/
protected Collection<Justification> getJustifications(KiWiReasoningConnection connection, KiWiTriple t, Set<Justification> transactionJustifications) throws SQLException {
HashSet<Justification> justifications = new HashSet<Justification>();
Iterations.addAll(connection.listJustificationsForTriple(t), justifications);
for(Justification j : transactionJustifications) {
if(equivalence.equivalent(j.getTriple(), t)) {
justifications.add(j);
}
}
return justifications;
}
/**
* For all justifications contained in the set passed as argument, create corresponding base justifications,
* i.e. justifications that only contain base triples and no inferred triples.
*
* @param justifications
* @return
*/
protected Set<Justification> getBaseJustifications(KiWiReasoningConnection connection, Set<Justification> justifications) throws SQLException, ReasoningException {
Set<Justification> baseJustifications = new HashSet<Justification>();
Map<KiWiTriple,Collection<Justification>> justificationCache = StatementCommons.newQuadrupleMap();
for(Justification justification : justifications) {
KiWiTriple triple = justification.getTriple();
Justification newJustification = new Justification();
newJustification.setSupportingRules(justification.getSupportingRules());
newJustification.setTriple(triple);
Set<Justification> tripleJustifications = Collections.singleton(newJustification);
// resolve inferred triples by replacing them by their justifications
for(KiWiTriple support : justification.getSupportingTriples()) {
if(support.isInferred()) {
Collection<Justification> supportJustifications = justificationCache.get(support);
// cache justifications of triple in case they are needed again in this run
if(supportJustifications == null || supportJustifications.size() == 0) {
supportJustifications = getJustifications(connection, support, baseJustifications);
justificationCache.put(support,supportJustifications);
}
if(supportJustifications.size() == 0) {
throw new UnjustifiedTripleException("error: inferred triple is not justified!", support);
}
// mix the two sets
Set<Justification> oldTripleJustifications = tripleJustifications;
tripleJustifications = new HashSet<Justification>();
for(Justification j1 : oldTripleJustifications) {
for(Justification j2 : supportJustifications) {
Justification j3 = new Justification();
j3.setTriple(triple);
j3.getSupportingTriples().addAll(j1.getSupportingTriples());
j3.getSupportingTriples().addAll(j2.getSupportingTriples());
j3.getSupportingRules().addAll(j1.getSupportingRules());
j3.getSupportingRules().addAll(j2.getSupportingRules());
tripleJustifications.add(j3);
}
}
} else {
for(Justification j : tripleJustifications) {
j.getSupportingTriples().add(support);
}
}
}
baseJustifications.addAll(tripleJustifications);
}
return baseJustifications;
}
/**
* The reasoner might create identical justifications in the process of generating the base justifications
* for a triple. This method removes duplicates at the expense of additional computation time.
* @param justifications
*/
private void removeDuplicateJustifications(KiWiReasoningConnection connection, Set<Justification> justifications) throws SQLException {
// remove duplicate justifications
Map<KiWiTriple,Collection<Justification>> justificationCache = StatementCommons.newQuadrupleMap();
for(Iterator<Justification> it = justifications.iterator(); it.hasNext(); ) {
Justification j = it.next();
Collection<Justification> supportJustifications = justificationCache.get(j.getTriple());
// cache justifications of triple in case they are needed again in this run
if(supportJustifications == null) {
supportJustifications = getJustifications(connection, j.getTriple(), Collections.<Justification>emptySet());
justificationCache.put(j.getTriple(),supportJustifications);
}
if(supportJustifications.contains(j)) {
it.remove();
}
}
}
protected static QueryResult matches(Pattern pattern, KiWiTriple triple) {
boolean result = true;
QueryResult match = new QueryResult();
if(pattern.getSubject().isResourceField()) {
result = ((ResourceField)pattern.getSubject()).getResource().equals(triple.getSubject());
} else if(pattern.getSubject().isVariableField()) {
KiWiNode binding = match.getBindings().get(pattern.getSubject());
if(binding != null) {
result = binding.equals(triple.getSubject());
} else {
match.getBindings().put((VariableField) pattern.getSubject(), triple.getSubject());
}
}
if(result && pattern.getProperty().isResourceField()) {
result = ((ResourceField)pattern.getProperty()).getResource().equals(triple.getPredicate());
} else if(result && pattern.getProperty().isVariableField()) {
KiWiNode binding = match.getBindings().get(pattern.getProperty());
if(binding != null) {
result = binding.equals(triple.getPredicate());
} else {
match.getBindings().put((VariableField) pattern.getProperty(), triple.getPredicate());
}
}
if(result && pattern.getContext() != null && pattern.getContext().isResourceField()) {
result = ((ResourceField)pattern.getContext()).getResource().equals(triple.getContext());
} else if(result && pattern.getContext() != null && pattern.getContext().isVariableField()) {
KiWiNode binding = match.getBindings().get(pattern.getContext());
if(binding != null) {
result = binding.equals(triple.getContext());
} else {
match.getBindings().put((VariableField) pattern.getContext(), triple.getContext());
}
}
if(result && pattern.getObject().isResourceField()) {
result = ((ResourceField)pattern.getObject()).getResource().equals(triple.getObject());
} else if(result && pattern.getObject().isLiteralField()) {
result = ((LiteralField)pattern.getObject()).getLiteral().equals(triple.getObject());
} else if(result && pattern.getObject().isVariableField()) {
KiWiNode binding = match.getBindings().get(pattern.getObject());
if(binding != null) {
result = binding.equals(triple.getObject());
} else {
match.getBindings().put((VariableField) pattern.getObject(), triple.getObject());
}
}
if(result) {
match.getJustifications().add(triple);
return match;
} else
return null;
}
/**
* Return true in case the reasoner is currently executing, false otherwise.
* @return
*/
public boolean isRunning() {
return reasonerThread.isRunning() || !reasoningQueue.isEmpty();
}
public void shutdown() {
shutdown(false);
}
public void shutdown(boolean force) {
if(isshutdown)
return;
if(force) {
log.warn("forced shutdown of reasoning service initiated, state will be inconsistent ...");
reasoningQueue.clear();
reasonerThread.shutdown(true);
for(int i = 0; i<5 && isRunning(); i++) {
log.warn("reasoner not yet finished, waiting for 100 ms (try={})", i+1);
try {
Thread.sleep(100);
} catch (InterruptedException e) {
}
}
// yes, I know it is unsafe; it is only used when forcefully shutting down on test ends before the database is deleted...
reasonerThread.stop();
} else {
log.info("graceful shutdown of reasoning service initiated ...");
for(int i = 0; i<20 && isRunning(); i++) {
log.warn("reasoner not yet finished, waiting for 1 seconds (try={})", i+1);
try {
Thread.sleep(1000);
} catch (InterruptedException e) {
}
}
reasonerThread.shutdown(false);
}
isshutdown = true;
}
/**
* Return the KiWiSailConnection underlying a given sail connection. The method will follow wrapped
* connections until it finds the KiWiSailConnection, or otherwise throws a SailException.
* @param connection
* @return
*/
private KiWiSailConnection getWrappedConnection(SailConnection connection) throws SailException {
SailConnection it = connection;
while(it instanceof SailConnectionWrapper) {
it = ((SailConnectionWrapper) it).getWrappedConnection();
if(it instanceof KiWiSailConnection) {
return (KiWiSailConnection) it;
}
}
throw new SailException("no underlying KiWiSailConnection found for connection");
}
private static int indexerCounter = 0;
private class SKWRLReasoner extends Thread {
private boolean shutdown = false;
private boolean running = false;
private boolean forceshutdown = false;
private SKWRLReasoner() {
super("SKWRL Reasoner " + ++indexerCounter);
setDaemon(true);
start();
}
public void shutdown(boolean force) {
log.info("REASONER: signalling shutdown to reasoner thread");
shutdown = true;
forceshutdown = force;
this.interrupt();
}
public boolean isRunning() {
return running;
}
@Override
public void run() {
log.info("{} starting up ...", getName());
startTask(getName(), TASK_GROUP);
while (!forceshutdown && (!shutdown || reasoningQueue.size() > 0)) {
running = false;
try {
updateTaskStatus("idle");
TransactionData data = reasoningQueue.take();
running = true;
updateTaskMaxProgress(reasoningQueue.size());
executeReasoner(data);
} catch (InterruptedException ex) {
} catch (RuntimeException ex) {
// can happen on forced shutdown
} catch (Exception ex) {
log.warn("reasoning task threw an exception",ex);
}
}
running = false;
try {
endTask();
} catch (Exception ex) {
}
log.info("{} shutting down ...", getName());
}
}
}