Repository: incubator-rya Updated Branches: refs/heads/master 4576f556a -> 7b571d43a
http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/7b571d43/sail/src/main/java/org/apache/rya/rdftriplestore/inference/InferenceEngine.java ---------------------------------------------------------------------- diff --git a/sail/src/main/java/org/apache/rya/rdftriplestore/inference/InferenceEngine.java b/sail/src/main/java/org/apache/rya/rdftriplestore/inference/InferenceEngine.java index 23fda51..86359f0 100644 --- a/sail/src/main/java/org/apache/rya/rdftriplestore/inference/InferenceEngine.java +++ b/sail/src/main/java/org/apache/rya/rdftriplestore/inference/InferenceEngine.java @@ -35,6 +35,10 @@ import java.util.Timer; import java.util.TimerTask; import java.util.TreeMap; import java.util.concurrent.ConcurrentHashMap; +import java.util.concurrent.atomic.AtomicBoolean; +import java.util.concurrent.atomic.AtomicLong; +import java.util.concurrent.atomic.AtomicReference; +import java.util.concurrent.locks.ReentrantLock; import org.apache.commons.lang3.mutable.MutableObject; import org.apache.log4j.Logger; @@ -76,35 +80,38 @@ public class InferenceEngine { private static final ValueFactory VF = ValueFactoryImpl.getInstance(); private static final URI HAS_SELF = VF.createURI(OWL.NAMESPACE, "hasSelf"); private static final URI REFLEXIVE_PROPERTY = VF.createURI(OWL.NAMESPACE, "ReflexiveProperty"); + public static final String URI_PROP = "uri"; - private Graph subClassOfGraph; - private Graph subPropertyOfGraph; - private Set<URI> symmetricPropertySet; - private Map<URI, URI> inverseOfMap; - private Set<URI> transitivePropertySet; - private Set<URI> reflexivePropertySet; - private Map<URI, Set<URI>> domainByType; - private Map<URI, Set<URI>> rangeByType; - private Map<Resource, Map<URI, Value>> hasValueByType; - private Map<URI, Map<Resource, Value>> hasValueByProperty; - private Map<Resource, Map<Resource, URI>> someValuesFromByRestrictionType; - private Map<Resource, Map<Resource, URI>> allValuesFromByValueType; - private final ConcurrentHashMap<Resource, List<Set<Resource>>> intersections = new ConcurrentHashMap<>(); - private final ConcurrentHashMap<Resource, Set<Resource>> enumerations = new ConcurrentHashMap<>(); + private final ReentrantLock refreshLock = new ReentrantLock(); + + private final AtomicReference<Graph> subClassOfGraph = new AtomicReference<>(); + private final AtomicReference<Graph> subPropertyOfGraph = new AtomicReference<>(); + + private final Set<URI> symmetricPropertySet = ConcurrentHashMap.newKeySet();; + private final Map<URI, URI> inverseOfMap = new ConcurrentHashMap<>(); + private final Set<URI> transitivePropertySet = ConcurrentHashMap.newKeySet();; + private final Set<URI> reflexivePropertySet = ConcurrentHashMap.newKeySet();; + private final Map<URI, Set<URI>> domainByType = new ConcurrentHashMap<>(); + private final Map<URI, Set<URI>> rangeByType = new ConcurrentHashMap<>(); + private final Map<Resource, Map<URI, Value>> hasValueByType = new ConcurrentHashMap<>(); + private final Map<URI, Map<Resource, Value>> hasValueByProperty = new ConcurrentHashMap<>(); + private final Map<Resource, Map<Resource, URI>> someValuesFromByRestrictionType = new ConcurrentHashMap<>(); + private final Map<Resource, Map<Resource, URI>> allValuesFromByValueType = new ConcurrentHashMap<>(); + private final Map<Resource, List<Set<Resource>>> intersections = new ConcurrentHashMap<>(); + private final Map<Resource, Set<Resource>> enumerations = new ConcurrentHashMap<>(); + private final Map<URI, List<URI>> propertyChainPropertyToChain = new ConcurrentHashMap<>(); // hasSelf maps. - private Map<URI, Set<Resource>> hasSelfByProperty; - private Map<Resource, Set<URI>> hasSelfByType; + private final Map<URI, Set<Resource>> hasSelfByProperty = new ConcurrentHashMap<>(); + private final Map<Resource, Set<URI>> hasSelfByType = new ConcurrentHashMap<>(); private RyaDAO<?> ryaDAO; private RdfCloudTripleStoreConfiguration conf; private RyaDaoQueryWrapper ryaDaoQueryWrapper; - private boolean initialized = false; - private boolean schedule = true; + private final AtomicBoolean isInitialized = new AtomicBoolean(); + private final AtomicBoolean schedule = new AtomicBoolean(true); - private long refreshGraphSchedule = 5 * 60 * 1000; //5 min + private final AtomicLong refreshGraphSchedule = new AtomicLong(5 * 60 * 1000); //5 min private Timer timer; - private HashMap<URI, List<URI>> propertyChainPropertyToChain = new HashMap<>(); - public static final String URI_PROP = "uri"; public void init() throws InferenceEngineException { try { @@ -117,11 +124,11 @@ public class InferenceEngine { checkArgument(ryaDAO.isInitialized(), "RdfDao is not initialized"); ryaDaoQueryWrapper = new RyaDaoQueryWrapper(ryaDAO, conf); - if (schedule) { - refreshGraph(); + refreshGraph(); + + if (schedule.get()) { timer = new Timer(InferenceEngine.class.getName()); timer.scheduleAtFixedRate(new TimerTask() { - @Override public void run() { try { @@ -130,10 +137,9 @@ public class InferenceEngine { throw new RuntimeException(e); } } - - }, refreshGraphSchedule, refreshGraphSchedule); + }, refreshGraphSchedule.get(), refreshGraphSchedule.get()); } - refreshGraph(); + setInitialized(true); } catch (final RyaDAOException e) { throw new InferenceEngineException(e); @@ -148,237 +154,51 @@ public class InferenceEngine { } public void refreshGraph() throws InferenceEngineException { + refreshLock.lock(); try { - CloseableIteration<Statement, QueryEvaluationException> iter; //get all subclassof Graph graph = TinkerGraph.open(); addPredicateEdges(RDFS.SUBCLASSOF, Direction.OUT, graph, RDFS.SUBCLASSOF.stringValue()); //equivalentClass is the same as subClassOf both ways addPredicateEdges(OWL.EQUIVALENTCLASS, Direction.BOTH, graph, RDFS.SUBCLASSOF.stringValue()); - // Add unions to the subclass graph: if c owl:unionOf LIST(c1, c2, ... cn), then any - // instances of c1, c2, ... or cn are also instances of c, meaning c is a superclass - // of all the rest. - // (In principle, an instance of c is likewise implied to be at least one of the other - // types, but this fact is ignored for now to avoid nondeterministic reasoning.) - iter = RyaDAOHelper.query(ryaDAO, null, OWL.UNIONOF, null, conf); - try { - while (iter.hasNext()) { - final Statement st = iter.next(); - final Value unionType = st.getSubject(); - // Traverse the list of types constituting the union - Value current = st.getObject(); - while (current instanceof Resource && !RDF.NIL.equals(current)) { - final Resource listNode = (Resource) current; - CloseableIteration<Statement, QueryEvaluationException> listIter = RyaDAOHelper.query(ryaDAO, - listNode, RDF.FIRST, null, conf); - try { - if (listIter.hasNext()) { - final Statement firstStatement = listIter.next(); - if (firstStatement.getObject() instanceof Resource) { - final Resource subclass = (Resource) firstStatement.getObject(); - final Statement subclassStatement = VF.createStatement(subclass, RDFS.SUBCLASSOF, unionType); - addStatementEdge(graph, RDFS.SUBCLASSOF.stringValue(), subclassStatement); - } - } - } finally { - listIter.close(); - } - listIter = RyaDAOHelper.query(ryaDAO, listNode, RDF.REST, null, conf); - try { - if (listIter.hasNext()) { - current = listIter.next().getObject(); - } - else { - current = RDF.NIL; - } - } finally { - listIter.close(); - } - } - } - } finally { - if (iter != null) { - iter.close(); - } - } - subClassOfGraph = graph; //TODO: Should this be synchronized? + // Add unions to the subclass graph + addUnions(graph); + subClassOfGraph.set(graph); graph = TinkerGraph.open(); addPredicateEdges(RDFS.SUBPROPERTYOF, Direction.OUT, graph, RDFS.SUBPROPERTYOF.stringValue()); //equiv property really is the same as a subPropertyOf both ways addPredicateEdges(OWL.EQUIVALENTPROPERTY, Direction.BOTH, graph, RDFS.SUBPROPERTYOF.stringValue()); - subPropertyOfGraph = graph; //TODO: Should this be synchronized? + subPropertyOfGraph.set(graph); refreshIntersectionOf(); refreshOneOf(); - symmetricPropertySet = fetchInstances(OWL.SYMMETRICPROPERTY); - transitivePropertySet = fetchInstances(OWL.TRANSITIVEPROPERTY); - reflexivePropertySet = fetchInstances(REFLEXIVE_PROPERTY); - - iter = RyaDAOHelper.query(ryaDAO, null, OWL.INVERSEOF, null, conf); - final Map<URI, URI> invProp = new HashMap<>(); - try { - while (iter.hasNext()) { - final Statement st = iter.next(); - invProp.put((URI) st.getSubject(), (URI) st.getObject()); - invProp.put((URI) st.getObject(), (URI) st.getSubject()); - } - } finally { - if (iter != null) { - iter.close(); - } + synchronized(symmetricPropertySet) { + symmetricPropertySet.clear(); + symmetricPropertySet.addAll(fetchInstances(OWL.SYMMETRICPROPERTY)); } - inverseOfMap = invProp; - - iter = RyaDAOHelper.query(ryaDAO, null, - VF.createURI("http://www.w3.org/2002/07/owl#propertyChainAxiom";), - null, conf); - final Map<URI,URI> propertyChainPropertiesToBNodes = new HashMap<>(); - propertyChainPropertyToChain = new HashMap<>(); - try { - while (iter.hasNext()){ - final Statement st = iter.next(); - propertyChainPropertiesToBNodes.put((URI)st.getSubject(), (URI)st.getObject()); - } - } finally { - if (iter != null) { - iter.close(); - } + synchronized(transitivePropertySet) { + transitivePropertySet.clear(); + transitivePropertySet.addAll(fetchInstances(OWL.TRANSITIVEPROPERTY)); } - // now for each property chain bNode, get the indexed list of properties associated with that chain - for (final URI propertyChainProperty : propertyChainPropertiesToBNodes.keySet()){ - final URI bNode = propertyChainPropertiesToBNodes.get(propertyChainProperty); - // query for the list of indexed properties - iter = RyaDAOHelper.query(ryaDAO, bNode, VF.createURI("http://www.w3.org/2000/10/swap/list#index";), - null, conf); - final TreeMap<Integer, URI> orderedProperties = new TreeMap<>(); - // TODO refactor this. Wish I could execute sparql - try { - while (iter.hasNext()){ - final Statement st = iter.next(); - final String indexedElement = st.getObject().stringValue(); - log.info(indexedElement); - CloseableIteration<Statement, QueryEvaluationException> iter2 = RyaDAOHelper.query(ryaDAO, VF.createURI(st.getObject().stringValue()), RDF.FIRST, - null, conf); - String integerValue = ""; - Value anonPropNode = null; - Value propURI = null; - if (iter2 != null){ - while (iter2.hasNext()){ - final Statement iter2Statement = iter2.next(); - integerValue = iter2Statement.getObject().stringValue(); - break; - } - iter2.close(); - } - iter2 = RyaDAOHelper.query(ryaDAO, VF.createURI(st.getObject().stringValue()), RDF.REST, - null, conf); - if (iter2 != null){ - while (iter2.hasNext()){ - final Statement iter2Statement = iter2.next(); - anonPropNode = iter2Statement.getObject(); - break; - } - iter2.close(); - if (anonPropNode != null){ - iter2 = RyaDAOHelper.query(ryaDAO, VF.createURI(anonPropNode.stringValue()), RDF.FIRST, - null, conf); - while (iter2.hasNext()){ - final Statement iter2Statement = iter2.next(); - propURI = iter2Statement.getObject(); - break; - } - iter2.close(); - } - } - if (!integerValue.isEmpty() && propURI!=null) { - try { - final int indexValue = Integer.parseInt(integerValue); - final URI chainPropURI = VF.createURI(propURI.stringValue()); - orderedProperties.put(indexValue, chainPropURI); - } - catch (final Exception ex){ - // TODO log an error here - - } - } - } - } finally{ - if (iter != null){ - iter.close(); - } - } - final List<URI> properties = new ArrayList<>(); - for (final Map.Entry<Integer, URI> entry : orderedProperties.entrySet()){ - properties.add(entry.getValue()); - } - propertyChainPropertyToChain.put(propertyChainProperty, properties); + synchronized(reflexivePropertySet) { + reflexivePropertySet.clear(); + reflexivePropertySet.addAll(fetchInstances(REFLEXIVE_PROPERTY)); } - // could also be represented as a list of properties (some of which may be blank nodes) - for (final URI propertyChainProperty : propertyChainPropertiesToBNodes.keySet()){ - final List<URI> existingChain = propertyChainPropertyToChain.get(propertyChainProperty); - // if we didn't get a chain, try to get it through following the collection - if ((existingChain == null) || existingChain.isEmpty()) { + refreshInverseOf(); - CloseableIteration<Statement, QueryEvaluationException> iter2 = RyaDAOHelper.query(ryaDAO, propertyChainPropertiesToBNodes.get(propertyChainProperty), RDF.FIRST, - null, conf); - final List<URI> properties = new ArrayList<>(); - URI previousBNode = propertyChainPropertiesToBNodes.get(propertyChainProperty); - if (iter2.hasNext()) { - Statement iter2Statement = iter2.next(); - Value currentPropValue = iter2Statement.getObject(); - while ((currentPropValue != null) && (!currentPropValue.stringValue().equalsIgnoreCase(RDF.NIL.stringValue()))){ - if (currentPropValue instanceof URI){ - iter2 = RyaDAOHelper.query(ryaDAO, VF.createURI(currentPropValue.stringValue()), RDF.FIRST, - null, conf); - if (iter2.hasNext()){ - iter2Statement = iter2.next(); - if (iter2Statement.getObject() instanceof URI){ - properties.add((URI)iter2Statement.getObject()); - } - } - // otherwise see if there is an inverse declaration - else { - iter2 = RyaDAOHelper.query(ryaDAO, VF.createURI(currentPropValue.stringValue()), OWL.INVERSEOF, - null, conf); - if (iter2.hasNext()){ - iter2Statement = iter2.next(); - if (iter2Statement.getObject() instanceof URI){ - properties.add(new InverseURI((URI)iter2Statement.getObject())); - } - } - } - // get the next prop pointer - iter2 = RyaDAOHelper.query(ryaDAO, previousBNode, RDF.REST, - null, conf); - if (iter2.hasNext()){ - iter2Statement = iter2.next(); - previousBNode = (URI)currentPropValue; - currentPropValue = iter2Statement.getObject(); - } - else { - currentPropValue = null; - } - } - else { - currentPropValue = null; - } - - } - propertyChainPropertyToChain.put(propertyChainProperty, properties); - } - } - } + refreshPropertyChainPropertyToChain(); refreshDomainRange(); refreshPropertyRestrictions(); - } catch (final QueryEvaluationException e) { throw new InferenceEngineException(e); + } finally { + refreshLock.unlock(); } } @@ -434,6 +254,227 @@ public class InferenceEngine { } /** + * Add unions to the subclass graph: if c owl:unionOf LIST(c1, c2, ... cn), + * then any instances of c1, c2, ... or cn are also instances of c, meaning + * c is a superclass of all the rest. + * (In principle, an instance of c is likewise implied to be at least one of + * the other types, but this fact is ignored for now to avoid + * nondeterministic reasoning.) + * @param graph the {@link Graph} to add to. + * @throws QueryEvaluationException + */ + private void addUnions(final Graph graph) throws QueryEvaluationException { + final CloseableIteration<Statement, QueryEvaluationException> iter = RyaDAOHelper.query(ryaDAO, null, OWL.UNIONOF, null, conf); + try { + while (iter.hasNext()) { + final Statement st = iter.next(); + final Value unionType = st.getSubject(); + // Traverse the list of types constituting the union + Value current = st.getObject(); + while (current instanceof Resource && !RDF.NIL.equals(current)) { + final Resource listNode = (Resource) current; + CloseableIteration<Statement, QueryEvaluationException> listIter = RyaDAOHelper.query(ryaDAO, + listNode, RDF.FIRST, null, conf); + try { + if (listIter.hasNext()) { + final Statement firstStatement = listIter.next(); + if (firstStatement.getObject() instanceof Resource) { + final Resource subclass = (Resource) firstStatement.getObject(); + final Statement subclassStatement = VF.createStatement(subclass, RDFS.SUBCLASSOF, unionType); + addStatementEdge(graph, RDFS.SUBCLASSOF.stringValue(), subclassStatement); + } + } + } finally { + listIter.close(); + } + listIter = RyaDAOHelper.query(ryaDAO, listNode, RDF.REST, null, conf); + try { + if (listIter.hasNext()) { + current = listIter.next().getObject(); + } + else { + current = RDF.NIL; + } + } finally { + listIter.close(); + } + } + } + } finally { + if (iter != null) { + iter.close(); + } + } + } + + private void refreshInverseOf() throws QueryEvaluationException { + final CloseableIteration<Statement, QueryEvaluationException> iter = RyaDAOHelper.query(ryaDAO, null, OWL.INVERSEOF, null, conf); + final Map<URI, URI> invProp = new HashMap<>(); + try { + while (iter.hasNext()) { + final Statement st = iter.next(); + invProp.put((URI) st.getSubject(), (URI) st.getObject()); + invProp.put((URI) st.getObject(), (URI) st.getSubject()); + } + } finally { + if (iter != null) { + iter.close(); + } + } + synchronized(inverseOfMap) { + inverseOfMap.clear(); + inverseOfMap.putAll(invProp); + } + } + + private void refreshPropertyChainPropertyToChain() throws QueryEvaluationException { + CloseableIteration<Statement, QueryEvaluationException> iter = RyaDAOHelper.query(ryaDAO, null, + VF.createURI("http://www.w3.org/2002/07/owl#propertyChainAxiom";), + null, conf); + final Map<URI,URI> propertyChainPropertiesToBNodes = new HashMap<>(); + final Map<URI, List<URI>> tempPropertyChainPropertyToChain = new HashMap<>(); + try { + while (iter.hasNext()){ + final Statement st = iter.next(); + propertyChainPropertiesToBNodes.put((URI)st.getSubject(), (URI)st.getObject()); + } + } finally { + if (iter != null) { + iter.close(); + } + } + // now for each property chain bNode, get the indexed list of properties associated with that chain + for (final URI propertyChainProperty : propertyChainPropertiesToBNodes.keySet()){ + final URI bNode = propertyChainPropertiesToBNodes.get(propertyChainProperty); + // query for the list of indexed properties + iter = RyaDAOHelper.query(ryaDAO, bNode, VF.createURI("http://www.w3.org/2000/10/swap/list#index";), + null, conf); + final TreeMap<Integer, URI> orderedProperties = new TreeMap<>(); + // TODO refactor this. Wish I could execute sparql + try { + while (iter.hasNext()){ + final Statement st = iter.next(); + final String indexedElement = st.getObject().stringValue(); + log.info(indexedElement); + CloseableIteration<Statement, QueryEvaluationException> iter2 = RyaDAOHelper.query(ryaDAO, VF.createURI(st.getObject().stringValue()), RDF.FIRST, + null, conf); + String integerValue = ""; + Value anonPropNode = null; + Value propURI = null; + if (iter2 != null){ + while (iter2.hasNext()){ + final Statement iter2Statement = iter2.next(); + integerValue = iter2Statement.getObject().stringValue(); + break; + } + iter2.close(); + } + iter2 = RyaDAOHelper.query(ryaDAO, VF.createURI(st.getObject().stringValue()), RDF.REST, + null, conf); + if (iter2 != null){ + while (iter2.hasNext()){ + final Statement iter2Statement = iter2.next(); + anonPropNode = iter2Statement.getObject(); + break; + } + iter2.close(); + if (anonPropNode != null){ + iter2 = RyaDAOHelper.query(ryaDAO, VF.createURI(anonPropNode.stringValue()), RDF.FIRST, + null, conf); + while (iter2.hasNext()){ + final Statement iter2Statement = iter2.next(); + propURI = iter2Statement.getObject(); + break; + } + iter2.close(); + } + } + if (!integerValue.isEmpty() && propURI!=null) { + try { + final int indexValue = Integer.parseInt(integerValue); + final URI chainPropURI = VF.createURI(propURI.stringValue()); + orderedProperties.put(indexValue, chainPropURI); + } + catch (final Exception e){ + log.error("Error adding chain property to ordered properties", e); + } + } + } + } finally{ + if (iter != null){ + iter.close(); + } + } + final List<URI> properties = new ArrayList<>(); + for (final Map.Entry<Integer, URI> entry : orderedProperties.entrySet()){ + properties.add(entry.getValue()); + } + tempPropertyChainPropertyToChain.put(propertyChainProperty, properties); + } + + // could also be represented as a list of properties (some of which may be blank nodes) + for (final URI propertyChainProperty : propertyChainPropertiesToBNodes.keySet()){ + final List<URI> existingChain = tempPropertyChainPropertyToChain.get(propertyChainProperty); + // if we didn't get a chain, try to get it through following the collection + if ((existingChain == null) || existingChain.isEmpty()) { + + CloseableIteration<Statement, QueryEvaluationException> iter2 = RyaDAOHelper.query(ryaDAO, propertyChainPropertiesToBNodes.get(propertyChainProperty), RDF.FIRST, + null, conf); + final List<URI> properties = new ArrayList<>(); + URI previousBNode = propertyChainPropertiesToBNodes.get(propertyChainProperty); + if (iter2.hasNext()) { + Statement iter2Statement = iter2.next(); + Value currentPropValue = iter2Statement.getObject(); + while ((currentPropValue != null) && (!currentPropValue.stringValue().equalsIgnoreCase(RDF.NIL.stringValue()))){ + if (currentPropValue instanceof URI){ + iter2 = RyaDAOHelper.query(ryaDAO, VF.createURI(currentPropValue.stringValue()), RDF.FIRST, + null, conf); + if (iter2.hasNext()){ + iter2Statement = iter2.next(); + if (iter2Statement.getObject() instanceof URI){ + properties.add((URI)iter2Statement.getObject()); + } + } + // otherwise see if there is an inverse declaration + else { + iter2 = RyaDAOHelper.query(ryaDAO, VF.createURI(currentPropValue.stringValue()), OWL.INVERSEOF, + null, conf); + if (iter2.hasNext()){ + iter2Statement = iter2.next(); + if (iter2Statement.getObject() instanceof URI){ + properties.add(new InverseURI((URI)iter2Statement.getObject())); + } + } + } + // get the next prop pointer + iter2 = RyaDAOHelper.query(ryaDAO, previousBNode, RDF.REST, + null, conf); + if (iter2.hasNext()){ + iter2Statement = iter2.next(); + previousBNode = (URI)currentPropValue; + currentPropValue = iter2Statement.getObject(); + } + else { + currentPropValue = null; + } + } + else { + currentPropValue = null; + } + + } + tempPropertyChainPropertyToChain.put(propertyChainProperty, properties); + } + } + } + + synchronized(propertyChainPropertyToChain) { + propertyChainPropertyToChain.clear(); + propertyChainPropertyToChain.putAll(tempPropertyChainPropertyToChain); + } + } + + /** * Queries domain and range information, then populates the inference engine with direct * domain/range relations and any that can be inferred from the subclass graph, subproperty * graph, and inverse property map. Should be called after that class and property information @@ -587,8 +628,14 @@ public class InferenceEngine { } } } - domainByType = domainByTypePartial; - rangeByType = rangeByTypePartial; + synchronized(domainByType) { + domainByType.clear(); + domainByType.putAll(domainByTypePartial); + } + synchronized(rangeByType) { + rangeByType.clear(); + rangeByType.putAll(rangeByTypePartial); + } } private void refreshPropertyRestrictions() throws QueryEvaluationException { @@ -613,8 +660,8 @@ public class InferenceEngine { } private void refreshHasValueRestrictions(final Map<Resource, URI> restrictions) throws QueryEvaluationException { - hasValueByType = new HashMap<>(); - hasValueByProperty = new HashMap<>(); + hasValueByType.clear(); + hasValueByProperty.clear(); final CloseableIteration<Statement, QueryEvaluationException> iter = RyaDAOHelper.query(ryaDAO, null, OWL.HASVALUE, null, conf); try { while (iter.hasNext()) { @@ -641,7 +688,7 @@ public class InferenceEngine { } private void refreshSomeValuesFromRestrictions(final Map<Resource, URI> restrictions) throws QueryEvaluationException { - someValuesFromByRestrictionType = new ConcurrentHashMap<>(); + someValuesFromByRestrictionType.clear(); ryaDaoQueryWrapper.queryAll(null, OWL.SOMEVALUESFROM, null, new RDFHandlerBase() { @Override public void handleStatement(final Statement statement) throws RDFHandlerException { @@ -667,7 +714,7 @@ public class InferenceEngine { } private void refreshAllValuesFromRestrictions(final Map<Resource, URI> restrictions) throws QueryEvaluationException { - allValuesFromByValueType = new ConcurrentHashMap<>(); + allValuesFromByValueType.clear(); ryaDaoQueryWrapper.queryAll(null, OWL.ALLVALUESFROM, null, new RDFHandlerBase() { @Override public void handleStatement(final Statement statement) throws RDFHandlerException { @@ -693,8 +740,8 @@ public class InferenceEngine { } private void refreshHasSelfRestrictions(final Map<Resource, URI> restrictions) throws QueryEvaluationException { - hasSelfByType = new HashMap<>(); - hasSelfByProperty = new HashMap<>(); + hasSelfByType.clear(); + hasSelfByProperty.clear(); for(final Resource type : restrictions.keySet()) { final URI property = restrictions.get(type); @@ -858,8 +905,10 @@ public class InferenceEngine { } }); - enumerations.clear(); - enumerations.putAll(enumTypes); + synchronized(enumerations) { + enumerations.clear(); + enumerations.putAll(enumTypes); + } } /** @@ -869,7 +918,7 @@ public class InferenceEngine { * * This takes into account type hierarchy, where children of a type that * have this property are also assumed to have the property. - * + * * @param type * The type (URI or bnode) to check against the known * restrictions @@ -887,7 +936,7 @@ public class InferenceEngine { } //findParent gets all subclasses, add self. if (type instanceof URI) { - for (final URI subtype : findParents(subClassOfGraph, (URI) type)) { + for (final URI subtype : findParents(subClassOfGraph.get(), (URI) type)) { tempProperties = hasSelfByType.get(subtype); if (tempProperties != null) { properties.addAll(tempProperties); @@ -915,11 +964,10 @@ public class InferenceEngine { if (baseTypes != null) { types.addAll(baseTypes); - // findParent gets all subclasses, add self. for (final Resource baseType : baseTypes) { if (baseType instanceof URI) { - types.addAll(findParents(subClassOfGraph, (URI) baseType)); + types.addAll(findParents(subClassOfGraph.get(), (URI) baseType)); } } } @@ -983,7 +1031,8 @@ public class InferenceEngine { private void addSubClassOf(final Resource s, final Resource o) { final Statement statement = new StatementImpl(s, RDFS.SUBCLASSOF, o); final String edgeName = RDFS.SUBCLASSOF.stringValue(); - addStatementEdge(subClassOfGraph, edgeName, statement); + + addStatementEdge(subClassOfGraph.get(), edgeName, statement); } private void addIntersection(final Set<Resource> intersection, final Resource type) { @@ -1032,7 +1081,7 @@ public class InferenceEngine { * or if either type or the subclass graph is {@code null}. */ public Set<URI> getSuperClasses(final URI type) { - return findChildren(subClassOfGraph, type); + return findChildren(subClassOfGraph.get(), type); } /** @@ -1044,7 +1093,7 @@ public class InferenceEngine { * or if either type or the subclass graph is {@code null}. */ public Set<URI> getSubClasses(final URI type) { - return findParents(subClassOfGraph, type); + return findParents(subClassOfGraph.get(), type); } /** @@ -1056,7 +1105,7 @@ public class InferenceEngine { * or if either property or the subproperty graph is {@code null}. */ public Set<URI> getSuperProperties(final URI property) { - return findChildren(subPropertyOfGraph, property); + return findChildren(subPropertyOfGraph.get(), property); } /** @@ -1068,7 +1117,7 @@ public class InferenceEngine { * or if either property or the subproperty graph is {@code null}. */ public Set<URI> getSubProperties(final URI property) { - return findParents(subPropertyOfGraph, property); + return findParents(subPropertyOfGraph.get(), property); } /** @@ -1283,32 +1332,32 @@ public class InferenceEngine { } public boolean isInitialized() { - return initialized; + return isInitialized.get(); } - public void setInitialized(final boolean initialized) { - this.initialized = initialized; + public void setInitialized(final boolean isInitialized) { + this.isInitialized.set(isInitialized); } - public RyaDAO<?> getRyaDAO() { + public synchronized RyaDAO<?> getRyaDAO() { return ryaDAO; } - public void setRyaDAO(final RyaDAO<?> ryaDAO) { + public synchronized void setRyaDAO(final RyaDAO<?> ryaDAO) { this.ryaDAO = ryaDAO; ryaDaoQueryWrapper = new RyaDaoQueryWrapper(ryaDAO); } - public RdfCloudTripleStoreConfiguration getConf() { + public synchronized RdfCloudTripleStoreConfiguration getConf() { return conf; } - public void setConf(final RdfCloudTripleStoreConfiguration conf) { + public synchronized void setConf(final RdfCloudTripleStoreConfiguration conf) { this.conf = conf; } public Graph getSubClassOfGraph() { - return subClassOfGraph; + return subClassOfGraph.get(); } public Map<URI, List<URI>> getPropertyChainMap() { @@ -1323,47 +1372,35 @@ public class InferenceEngine { } public Graph getSubPropertyOfGraph() { - return subPropertyOfGraph; + return subPropertyOfGraph.get(); } public long getRefreshGraphSchedule() { - return refreshGraphSchedule; + return refreshGraphSchedule.get(); } public void setRefreshGraphSchedule(final long refreshGraphSchedule) { - this.refreshGraphSchedule = refreshGraphSchedule; + this.refreshGraphSchedule.set(refreshGraphSchedule); } public Set<URI> getSymmetricPropertySet() { return symmetricPropertySet; } - public void setSymmetricPropertySet(final Set<URI> symmetricPropertySet) { - this.symmetricPropertySet = symmetricPropertySet; - } - public Map<URI, URI> getInverseOfMap() { return inverseOfMap; } - public void setInverseOfMap(final Map<URI, URI> inverseOfMap) { - this.inverseOfMap = inverseOfMap; - } - public Set<URI> getTransitivePropertySet() { return transitivePropertySet; } - public void setTransitivePropertySet(final Set<URI> transitivePropertySet) { - this.transitivePropertySet = transitivePropertySet; - } - public boolean isSchedule() { - return schedule; + return schedule.get(); } public void setSchedule(final boolean schedule) { - this.schedule = schedule; + this.schedule.set(schedule); } /** @@ -1532,7 +1569,7 @@ public class InferenceEngine { * to the restriction type. Empty map if the parameter is {@code null} or if the * someValuesFrom schema has not been populated. */ - public Map<Resource, Set<URI>> getSomeValuesFromByRestrictionType(Resource restrictionType) { + public Map<Resource, Set<URI>> getSomeValuesFromByRestrictionType(final Resource restrictionType) { return getTypePropertyImplyingType(restrictionType, someValuesFromByRestrictionType); } http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/7b571d43/sail/src/main/java/org/apache/rya/rdftriplestore/inference/PropertyChainVisitor.java ---------------------------------------------------------------------- diff --git a/sail/src/main/java/org/apache/rya/rdftriplestore/inference/PropertyChainVisitor.java b/sail/src/main/java/org/apache/rya/rdftriplestore/inference/PropertyChainVisitor.java index 251aa0c..ae7e059 100644 --- a/sail/src/main/java/org/apache/rya/rdftriplestore/inference/PropertyChainVisitor.java +++ b/sail/src/main/java/org/apache/rya/rdftriplestore/inference/PropertyChainVisitor.java @@ -83,6 +83,9 @@ public class PropertyChainVisitor extends AbstractInferVisitor { nextSubj = currentObj; } + if (lastStatementPatternAdded == null) { + throw new NullPointerException("lastStatementPatternAdded is null despite non-empty inferenceEngine property chain. chain.size()==" + chain.size()); + } lastStatementPatternAdded.setObjectVar(originalObj); TupleExpr lastRight = null; http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/7b571d43/sail/src/main/java/org/apache/rya/rdftriplestore/namespace/NamespaceManager.java ---------------------------------------------------------------------- diff --git a/sail/src/main/java/org/apache/rya/rdftriplestore/namespace/NamespaceManager.java b/sail/src/main/java/org/apache/rya/rdftriplestore/namespace/NamespaceManager.java index 3664d64..3d8526f 100644 --- a/sail/src/main/java/org/apache/rya/rdftriplestore/namespace/NamespaceManager.java +++ b/sail/src/main/java/org/apache/rya/rdftriplestore/namespace/NamespaceManager.java @@ -1,5 +1,14 @@ package org.apache.rya.rdftriplestore.namespace; +import java.io.InputStream; + +import org.apache.rya.api.RdfCloudTripleStoreConfiguration; +import org.apache.rya.api.persist.RdfDAOException; +import org.apache.rya.api.persist.RyaDAO; +import org.apache.rya.api.persist.RyaNamespaceManager; +import org.openrdf.model.Namespace; +import org.openrdf.sail.SailException; + /* * Licensed to the Apache Software Foundation (ASF) under one * or more contributor license agreements. See the NOTICE file @@ -22,18 +31,10 @@ package org.apache.rya.rdftriplestore.namespace; import info.aduna.iteration.CloseableIteration; -import org.apache.rya.api.RdfCloudTripleStoreConfiguration; -import org.apache.rya.api.persist.RdfDAOException; -import org.apache.rya.api.persist.RyaDAO; -import org.apache.rya.api.persist.RyaNamespaceManager; import net.sf.ehcache.Cache; import net.sf.ehcache.CacheManager; import net.sf.ehcache.Element; import net.sf.ehcache.Statistics; -import org.openrdf.model.Namespace; -import org.openrdf.sail.SailException; - -import java.io.InputStream; /** * Class NamespaceManager @@ -53,10 +54,9 @@ public class NamespaceManager { } protected void initialize(RyaDAO ryaDAO) { - try { - this.namespaceManager = ryaDAO.getNamespaceManager(); + this.namespaceManager = ryaDAO.getNamespaceManager(); - InputStream cacheConfigStream = Thread.currentThread().getContextClassLoader().getResourceAsStream("ehcache.xml"); + try (InputStream cacheConfigStream = Thread.currentThread().getContextClassLoader().getResourceAsStream("ehcache.xml")) { if (cacheConfigStream == null) { this.cacheManager = CacheManager.create(); // throw new RuntimeException("Cache Configuration does not exist"); http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/7b571d43/web/web.rya/resources/environment.properties ---------------------------------------------------------------------- diff --git a/web/web.rya/resources/environment.properties b/web/web.rya/resources/environment.properties deleted file mode 100644 index 2a9ffe7..0000000 --- a/web/web.rya/resources/environment.properties +++ /dev/null @@ -1,27 +0,0 @@ -# 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. - -instance.name=cloudbase -instance.zk=localhost:2181 -instance.username=root -instance.password=secret -rya.tableprefix=triplestore_ -rya.displayqueryplan=true -mongo.db.collectionprefix=rya_ -mongo.db.instance=localhost -mongo.db.name=rya -mongo.db.port=27017 http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/7b571d43/web/web.rya/src/main/java/org/apache/cloud/rdf/web/sail/RdfController.java ---------------------------------------------------------------------- diff --git a/web/web.rya/src/main/java/org/apache/cloud/rdf/web/sail/RdfController.java b/web/web.rya/src/main/java/org/apache/cloud/rdf/web/sail/RdfController.java index 93c5972..209c2b4 100644 --- a/web/web.rya/src/main/java/org/apache/cloud/rdf/web/sail/RdfController.java +++ b/web/web.rya/src/main/java/org/apache/cloud/rdf/web/sail/RdfController.java @@ -8,9 +8,9 @@ package org.apache.cloud.rdf.web.sail; * 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 @@ -34,10 +34,12 @@ import javax.servlet.ServletOutputStream; import javax.servlet.http.HttpServletRequest; import javax.servlet.http.HttpServletResponse; -import org.apache.rya.api.security.SecurityProvider; +import org.apache.commons.lang3.StringEscapeUtils; +import org.apache.log4j.Logger; import org.apache.rya.api.RdfCloudTripleStoreConfiguration; +import org.apache.rya.api.log.LogUtils; +import org.apache.rya.api.security.SecurityProvider; import org.apache.rya.rdftriplestore.RdfCloudTripleStoreConnection; - import org.openrdf.model.Resource; import org.openrdf.model.Statement; import org.openrdf.query.BindingSet; @@ -82,58 +84,57 @@ import org.springframework.web.bind.annotation.RequestParam; */ @Controller public class RdfController { - - private static final int QUERY_TIME_OUT_SECONDS = 120; + private static final Logger log = Logger.getLogger(RdfController.class); + + private static final int QUERY_TIME_OUT_SECONDS = 120; @Autowired SailRepository repository; - - @Autowired + + @Autowired SecurityProvider provider; @RequestMapping(value = "/queryrdf", method = {RequestMethod.GET, RequestMethod.POST}) - public void queryRdf(@RequestParam("query") String query, + public void queryRdf(@RequestParam("query") final String query, @RequestParam(value = RdfCloudTripleStoreConfiguration.CONF_QUERY_AUTH, required = false) String auth, - @RequestParam(value = RdfCloudTripleStoreConfiguration.CONF_CV, required = false) String vis, - @RequestParam(value = RdfCloudTripleStoreConfiguration.CONF_INFER, required = false) String infer, - @RequestParam(value = "nullout", required = false) String nullout, - @RequestParam(value = RdfCloudTripleStoreConfiguration.CONF_RESULT_FORMAT, required = false) String emit, - @RequestParam(value = "padding", required = false) String padding, - @RequestParam(value = "callback", required = false) String callback, - HttpServletRequest request, - HttpServletResponse response) { + @RequestParam(value = RdfCloudTripleStoreConfiguration.CONF_CV, required = false) final String vis, + @RequestParam(value = RdfCloudTripleStoreConfiguration.CONF_INFER, required = false) final String infer, + @RequestParam(value = "nullout", required = false) final String nullout, + @RequestParam(value = RdfCloudTripleStoreConfiguration.CONF_RESULT_FORMAT, required = false) final String emit, + @RequestParam(value = "padding", required = false) final String padding, + @RequestParam(value = "callback", required = false) final String callback, + final HttpServletRequest request, + final HttpServletResponse response) { + // WARNING: if you add to the above request variables, + // Be sure to validate and encode since they come from the outside and could contain odd damaging character sequences. SailRepositoryConnection conn = null; - final Thread queryThread = Thread.currentThread(); - auth = StringUtils.arrayToCommaDelimitedString(provider.getUserAuths(request)); - Timer timer = new Timer(); - timer.schedule(new TimerTask() { - - @Override - public void run() { - System.out.println("interrupting"); - queryThread.interrupt(); - - } - }, QUERY_TIME_OUT_SECONDS * 1000); - - try { - ServletOutputStream os = response.getOutputStream(); - conn = repository.getConnection(); + final Thread queryThread = Thread.currentThread(); + auth = StringUtils.arrayToCommaDelimitedString(provider.getUserAuths(request)); + final Timer timer = new Timer(); + timer.schedule(new TimerTask() { - Boolean isBlankQuery = StringUtils.isEmpty(query); - ParsedOperation operation = QueryParserUtil.parseOperation(QueryLanguage.SPARQL, query, null); + @Override + public void run() { + log.debug("interrupting"); + queryThread.interrupt(); - Boolean requestedCallback = !StringUtils.isEmpty(callback); - Boolean requestedFormat = !StringUtils.isEmpty(emit); - - if (requestedCallback) { - os.print(callback + "("); } + }, QUERY_TIME_OUT_SECONDS * 1000); + + try { + final ServletOutputStream os = response.getOutputStream(); + conn = repository.getConnection(); + + final Boolean isBlankQuery = StringUtils.isEmpty(query); + final ParsedOperation operation = QueryParserUtil.parseOperation(QueryLanguage.SPARQL, query, null); + + final Boolean requestedCallback = !StringUtils.isEmpty(callback); + final Boolean requestedFormat = !StringUtils.isEmpty(emit); if (!isBlankQuery) { - if (operation instanceof ParsedGraphQuery) { - // Perform Graph Query - RDFHandler handler = new RDFXMLWriter(os); + if (operation instanceof ParsedGraphQuery) { + // Perform Graph Query + final RDFHandler handler = new RDFXMLWriter(os); response.setContentType("text/xml"); performGraphQuery(query, conn, auth, infer, nullout, handler); } else if (operation instanceof ParsedTupleQuery) { @@ -160,33 +161,35 @@ public class RdfController { if (requestedCallback) { os.print(")"); } - } catch (Exception e) { - e.printStackTrace(); + } catch (final Exception e) { + log.error("Error running query", e); throw new RuntimeException(e); } finally { if (conn != null) { try { conn.close(); - } catch (RepositoryException e) { - e.printStackTrace(); + } catch (final RepositoryException e) { + log.error("Error closing connection", e); } } } - - timer.cancel(); + + timer.cancel(); } - - private void performQuery(String query, RepositoryConnection conn, String auth, String infer, String nullout, TupleQueryResultHandler handler) throws RepositoryException, MalformedQueryException, QueryEvaluationException, TupleQueryResultHandlerException { - TupleQuery tupleQuery = conn.prepareTupleQuery(QueryLanguage.SPARQL, query); - if (auth != null && auth.length() > 0) + + private void performQuery(final String query, final RepositoryConnection conn, final String auth, final String infer, final String nullout, final TupleQueryResultHandler handler) throws RepositoryException, MalformedQueryException, QueryEvaluationException, TupleQueryResultHandlerException { + final TupleQuery tupleQuery = conn.prepareTupleQuery(QueryLanguage.SPARQL, query); + if (auth != null && auth.length() > 0) { tupleQuery.setBinding(RdfCloudTripleStoreConfiguration.CONF_QUERY_AUTH, VALUE_FACTORY.createLiteral(auth)); - if (infer != null && infer.length() > 0) + } + if (infer != null && infer.length() > 0) { tupleQuery.setBinding(RdfCloudTripleStoreConfiguration.CONF_INFER, VALUE_FACTORY.createLiteral(Boolean.parseBoolean(infer))); + } if (nullout != null && nullout.length() > 0) { //output nothing, but still run query tupleQuery.evaluate(new TupleQueryResultHandler() { @Override - public void startQueryResult(List<String> strings) throws TupleQueryResultHandlerException { + public void startQueryResult(final List<String> strings) throws TupleQueryResultHandlerException { } @Override @@ -194,147 +197,155 @@ public class RdfController { } @Override - public void handleSolution(BindingSet bindings) throws TupleQueryResultHandlerException { + public void handleSolution(final BindingSet bindings) throws TupleQueryResultHandlerException { } @Override - public void handleBoolean(boolean arg0) throws QueryResultHandlerException { + public void handleBoolean(final boolean arg0) throws QueryResultHandlerException { } @Override - public void handleLinks(List<String> arg0) throws QueryResultHandlerException { + public void handleLinks(final List<String> arg0) throws QueryResultHandlerException { } }); } else { - CountingTupleQueryResultHandlerWrapper sparqlWriter = new CountingTupleQueryResultHandlerWrapper(handler); - long startTime = System.currentTimeMillis(); + final CountingTupleQueryResultHandlerWrapper sparqlWriter = new CountingTupleQueryResultHandlerWrapper(handler); + final long startTime = System.currentTimeMillis(); tupleQuery.evaluate(sparqlWriter); - System.out.format("Query Time = %.3f\n", (System.currentTimeMillis() - startTime) / 1000.); - System.out.format("Result Count = %s\n", sparqlWriter.getCount()); + log.info(String.format("Query Time = %.3f\n", (System.currentTimeMillis() - startTime) / 1000.)); + log.info(String.format("Result Count = %s\n", sparqlWriter.getCount())); } } - - private void performGraphQuery(String query, RepositoryConnection conn, String auth, String infer, String nullout, RDFHandler handler) throws RepositoryException, MalformedQueryException, QueryEvaluationException, RDFHandlerException { - GraphQuery graphQuery = conn.prepareGraphQuery(QueryLanguage.SPARQL, query); - if (auth != null && auth.length() > 0) - graphQuery.setBinding(RdfCloudTripleStoreConfiguration.CONF_QUERY_AUTH, VALUE_FACTORY.createLiteral(auth)); - if (infer != null && infer.length() > 0) - graphQuery.setBinding(RdfCloudTripleStoreConfiguration.CONF_INFER, VALUE_FACTORY.createLiteral(Boolean.parseBoolean(infer))); + + private void performGraphQuery(final String query, final RepositoryConnection conn, final String auth, final String infer, final String nullout, final RDFHandler handler) throws RepositoryException, MalformedQueryException, QueryEvaluationException, RDFHandlerException { + final GraphQuery graphQuery = conn.prepareGraphQuery(QueryLanguage.SPARQL, query); + if (auth != null && auth.length() > 0) { + graphQuery.setBinding(RdfCloudTripleStoreConfiguration.CONF_QUERY_AUTH, VALUE_FACTORY.createLiteral(auth)); + } + if (infer != null && infer.length() > 0) { + graphQuery.setBinding(RdfCloudTripleStoreConfiguration.CONF_INFER, VALUE_FACTORY.createLiteral(Boolean.parseBoolean(infer))); + } if (nullout != null && nullout.length() > 0) { //output nothing, but still run query - // TODO this seems like a strange use case. - graphQuery.evaluate(new RDFHandler() { - @Override - public void startRDF() throws RDFHandlerException { - } - - @Override - public void endRDF() throws RDFHandlerException { - } - - @Override - public void handleNamespace(String prefix, String uri) - throws RDFHandlerException { - } - - @Override - public void handleStatement(Statement st) - throws RDFHandlerException { - } - - @Override - public void handleComment(String comment) - throws RDFHandlerException { - } + // TODO this seems like a strange use case. + graphQuery.evaluate(new RDFHandler() { + @Override + public void startRDF() throws RDFHandlerException { + } + + @Override + public void endRDF() throws RDFHandlerException { + } + + @Override + public void handleNamespace(final String prefix, final String uri) + throws RDFHandlerException { + } + + @Override + public void handleStatement(final Statement st) + throws RDFHandlerException { + } + + @Override + public void handleComment(final String comment) + throws RDFHandlerException { + } }); } else { - long startTime = System.currentTimeMillis(); + final long startTime = System.currentTimeMillis(); graphQuery.evaluate(handler); - System.out.format("Query Time = %.3f\n", (System.currentTimeMillis() - startTime) / 1000.); + log.info(String.format("Query Time = %.3f\n", (System.currentTimeMillis() - startTime) / 1000.)); } } - private void performUpdate(String query, SailRepositoryConnection conn, ServletOutputStream os, String infer, String vis) throws RepositoryException, MalformedQueryException, IOException { - Update update = conn.prepareUpdate(QueryLanguage.SPARQL, query); - if (infer != null && infer.length() > 0) + private void performUpdate(final String query, final SailRepositoryConnection conn, final ServletOutputStream os, final String infer, final String vis) throws RepositoryException, MalformedQueryException, IOException { + final Update update = conn.prepareUpdate(QueryLanguage.SPARQL, query); + if (infer != null && infer.length() > 0) { update.setBinding(RdfCloudTripleStoreConfiguration.CONF_INFER, VALUE_FACTORY.createLiteral(Boolean.parseBoolean(infer))); + } if (conn.getSailConnection() instanceof RdfCloudTripleStoreConnection && vis != null) { - RdfCloudTripleStoreConnection sailConnection = (RdfCloudTripleStoreConnection) conn.getSailConnection(); + final RdfCloudTripleStoreConnection<?> sailConnection = (RdfCloudTripleStoreConnection<?>) conn.getSailConnection(); sailConnection.getConf().set(RdfCloudTripleStoreConfiguration.CONF_CV, vis); } - long startTime = System.currentTimeMillis(); + final long startTime = System.currentTimeMillis(); try { update.execute(); - } catch (UpdateExecutionException e) { - os.print(String.format("Update could not be successfully completed for query: %s\n\n", query)); - os.print(String.format("\n\n%s", e.getLocalizedMessage())); + } catch (final UpdateExecutionException e) { + final String message = "Update could not be successfully completed for query: "; + os.print(String.format(message + "%s\n\n", StringEscapeUtils.escapeHtml4(query))); + log.error(message + LogUtils.clean(query), e); } - System.out.format("Update Time = %.3f\n", (System.currentTimeMillis() - startTime) / 1000.); - } - + log.info(String.format("Update Time = %.3f\n", (System.currentTimeMillis() - startTime) / 1000.)); + } + private static final class CountingTupleQueryResultHandlerWrapper implements TupleQueryResultHandler { - private TupleQueryResultHandler indir; - private int count = 0; - - public CountingTupleQueryResultHandlerWrapper(TupleQueryResultHandler indir){ - this.indir = indir; - } - - public int getCount() { return count; } - - @Override - public void endQueryResult() throws TupleQueryResultHandlerException { - indir.endQueryResult(); - } - - @Override - public void handleSolution(BindingSet bindingSet) throws TupleQueryResultHandlerException { - count++; - indir.handleSolution(bindingSet); - } - @Override - public void startQueryResult(List<String> bindingNames) throws TupleQueryResultHandlerException { - count = 0; - indir.startQueryResult(bindingNames); - } - - @Override - public void handleBoolean(boolean arg0) throws QueryResultHandlerException { - } - - @Override - public void handleLinks(List<String> arg0) throws QueryResultHandlerException { - } + private final TupleQueryResultHandler indir; + private int count = 0; + + public CountingTupleQueryResultHandlerWrapper(final TupleQueryResultHandler indir){ + this.indir = indir; + } + + public int getCount() { + return count; + } + + @Override + public void endQueryResult() throws TupleQueryResultHandlerException { + indir.endQueryResult(); + } + + @Override + public void handleSolution(final BindingSet bindingSet) throws TupleQueryResultHandlerException { + count++; + indir.handleSolution(bindingSet); + } + + @Override + public void startQueryResult(final List<String> bindingNames) throws TupleQueryResultHandlerException { + count = 0; + indir.startQueryResult(bindingNames); + } + + @Override + public void handleBoolean(final boolean arg0) throws QueryResultHandlerException { + } + + @Override + public void handleLinks(final List<String> arg0) throws QueryResultHandlerException { + } } @RequestMapping(value = "/loadrdf", method = RequestMethod.POST) - public void loadRdf(@RequestParam(required = false) String format, - @RequestParam(value = RdfCloudTripleStoreConfiguration.CONF_CV, required = false) String cv, - @RequestParam(required = false) String graph, - @RequestBody String body, - HttpServletResponse response) + public void loadRdf(@RequestParam(required = false) final String format, + @RequestParam(value = RdfCloudTripleStoreConfiguration.CONF_CV, required = false) final String cv, + @RequestParam(required = false) final String graph, + @RequestBody final String body, + final HttpServletResponse response) throws RepositoryException, IOException, RDFParseException { - List<Resource> authList = new ArrayList<Resource>(); + final List<Resource> authList = new ArrayList<Resource>(); RDFFormat format_r = RDFFormat.RDFXML; if (format != null) { format_r = RDFFormat.valueOf(format); - if (format_r == null) + if (format_r == null) { throw new RuntimeException("RDFFormat[" + format + "] not found"); + } } if (graph != null) { - authList.add(VALUE_FACTORY.createURI(graph)); + authList.add(VALUE_FACTORY.createURI(graph)); } SailRepositoryConnection conn = null; try { conn = repository.getConnection(); - + if (conn.getSailConnection() instanceof RdfCloudTripleStoreConnection && cv != null) { - RdfCloudTripleStoreConnection sailConnection = (RdfCloudTripleStoreConnection) conn.getSailConnection(); + final RdfCloudTripleStoreConnection<?> sailConnection = (RdfCloudTripleStoreConnection<?>) conn.getSailConnection(); sailConnection.getConf().set(RdfCloudTripleStoreConfiguration.CONF_CV, cv); } http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/7b571d43/web/web.rya/src/main/webapp/sparqlQuery.jsp ---------------------------------------------------------------------- diff --git a/web/web.rya/src/main/webapp/sparqlQuery.jsp b/web/web.rya/src/main/webapp/sparqlQuery.jsp index a787b81..947a2db 100644 --- a/web/web.rya/src/main/webapp/sparqlQuery.jsp +++ b/web/web.rya/src/main/webapp/sparqlQuery.jsp @@ -20,16 +20,22 @@ under the License. <%@ page contentType="text/html; charset=iso-8859-1" language="java" %> <%@ page import="java.net.*" %> <% - String sparql=request.getParameter("sparql"); - String infer=request.getParameter("infer"); - String auth=request.getParameter("auth"); - String vis=request.getParameter("vis"); - String resultFormat = request.getParameter("emit"); - String padding = request.getParameter("padding"); + String x; + String sparql=(x=request.getParameter("sparql"))==null?"":x; + + if(sparql.length() > 0 ) { + String infer = (x=request.getParameter("infer"))==null?"":x; + String auth = (x=request.getParameter("auth"))==null?"":x; + String vis = (x=request.getParameter("vis"))==null?"":x; + String resultFormat = (x=request.getParameter("emit"))==null?"":x; + + String urlTo = // + "queryrdf?query.infer="+URLEncoder.encode(infer,"UTF-8") // + +"&query.auth="+URLEncoder.encode(auth,"UTF-8") // + +"&conf.cv="+URLEncoder.encode(vis,"UTF-8") // + +"&query.resultformat="+URLEncoder.encode(resultFormat,"UTF-8") // + +"&query="+URLEncoder.encode(sparql,"UTF-8"); - if(sparql != null){ - String sparqlEnc = URLEncoder.encode(sparql,"UTF-8"); - String urlTo = "queryrdf?query.infer="+infer+"&query.auth="+auth+"&conf.cv="+vis+"&query.resultformat="+resultFormat+"&padding="+padding+"&query="+sparqlEnc; response.sendRedirect(urlTo); } %> @@ -43,9 +49,7 @@ under the License. </tr> <tr> <td>SPARQL Query: </td> - <td><textarea cols="150" rows="50" name="sparql"> -Enter Sparql query here - </textarea></td> + <td><textarea cols="150" rows="50" name="sparql" placeholder="Enter SPARQL query here"></textarea></td> </tr> <tr> <td>Inferencing?(true/false)</td> @@ -66,10 +70,6 @@ Enter Sparql query here <option value="json">JSON</option> </select></td> </tr> - <tr> - <td>JSONP Padding</td> - <td><input type=text name="padding" size="20"></td> - </tr> <tr> <td> </td> <td><input type="submit" name="submit" value="Submit"></td> http://git-wip-us.apache.org/repos/asf/incubator-rya/blob/7b571d43/web/web.rya/src/test/java/org/apache/cloud/rdf/web/sail/RdfControllerTest.java ---------------------------------------------------------------------- diff --git a/web/web.rya/src/test/java/org/apache/cloud/rdf/web/sail/RdfControllerTest.java b/web/web.rya/src/test/java/org/apache/cloud/rdf/web/sail/RdfControllerTest.java index a09c9b1..f69de61 100644 --- a/web/web.rya/src/test/java/org/apache/cloud/rdf/web/sail/RdfControllerTest.java +++ b/web/web.rya/src/test/java/org/apache/cloud/rdf/web/sail/RdfControllerTest.java @@ -8,9 +8,9 @@ package org.apache.cloud.rdf.web.sail; * 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 @@ -19,15 +19,15 @@ package org.apache.cloud.rdf.web.sail; * under the License. */ - - -import static org.hamcrest.Matchers.equalToIgnoringWhiteSpace; +import static org.hamcrest.Matchers.containsString; +import static org.hamcrest.Matchers.not; import static org.junit.Assert.assertTrue; import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get; import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.content; import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status; import static org.springframework.test.web.servlet.setup.MockMvcBuilders.standaloneSetup; +import org.apache.rya.api.RdfCloudTripleStoreConfiguration; import org.junit.Before; import org.junit.Rule; import org.junit.Test; @@ -111,16 +111,49 @@ public class RdfControllerTest { .andExpect(status().isOk()) .andExpect(content().contentType(MediaType.TEXT_XML)); } - + + /** + * Make sure input variables with odd characters that could be json get encoded. + * literals should be represented correctly, for example: "bad" in JSON becomes \"bad\" (java escaped \\\"bad\\\") + * + * @throws Exception + */ @Test - public void callback() throws Exception { - this.mockMvc.perform(get("/queryrdf") - .param("query", "") - .param("callback", "test")) - .andExpect(status().isOk()) - .andExpect(content().string(equalToIgnoringWhiteSpace("test()"))); + public void callbackEncodeCorrectlyJson() throws Exception { + this.mockMvc.perform(get("/queryrdf") // + .param("query", "select ?x where { BIND( '''testbad\\\\or\"bad\"''' AS ?x) }") // + .param(RdfCloudTripleStoreConfiguration.CONF_QUERY_AUTH , "test<bad>or{bad}or\"bad\"") // + .param(RdfCloudTripleStoreConfiguration.CONF_CV , "test<bad>or{bad}or\"bad\"") // + .param(RdfCloudTripleStoreConfiguration.CONF_INFER , "test<bad>or{bad}or\"bad\"") // + .param(RdfCloudTripleStoreConfiguration.CONF_RESULT_FORMAT, "json")) // + .andExpect(content().string(not(containsString("<bad>")))) // non-query param data should not be in the results + .andExpect(content().string(not(containsString("{bad}")))) // non-query param data should not be in the results + .andExpect(content().string(not(containsString("bad\\or")))) // should be bad\\\\or + .andExpect(content().string(not(containsString("\"bad\"")))); // should be \\\"bad\\\" } + /** + * Make sure input variables with odd characters that could be xml get encoded. + * literals should be represented correctly, for example: <bad> in xml becomes <bad> + * + * @throws Exception + */ +@Test + public void encodeCorrectlyXml() throws Exception { + this.mockMvc.perform(get("/queryrdf") // + .param("query", "select ?x where { BIND( '''test<bad>or&bador'bador"bad"''' AS ?x ) }") // + .param(RdfCloudTripleStoreConfiguration.CONF_QUERY_AUTH , "test<bad>or{bad}or\"bad\"") // + .param(RdfCloudTripleStoreConfiguration.CONF_CV , "test<bad>or{bad}or\"bad\"") // + .param(RdfCloudTripleStoreConfiguration.CONF_INFER , "test<bad>or{bad}or\"bad\"") // + .param(RdfCloudTripleStoreConfiguration.CONF_RESULT_FORMAT, "test<bad>or{bad}or\"bad\"")) // + .andExpect(content().string(not(containsString("<bad")))) // < + .andExpect(content().string(not(containsString("bad>")))) // > + .andExpect(content().string(not(containsString("{bad}"))))// non-query param data should not be in the results + .andExpect(content().string(not(containsString("&bad")))) // & + .andExpect(content().string(not(containsString("'bad")))) // &apos; converted from ' + .andExpect(content().string(not(containsString("\"bad")))); // &" converted from " +} + @Test public void malformedQuery() throws Exception { thrown.expect(NestedServletException.class); @@ -131,7 +164,7 @@ public class RdfControllerTest { @Test public void updateQuery() throws Exception { this.mockMvc.perform(get("/queryrdf") - .param("query", "INSERT DATA { <http://mynamespace/ProductType1> <http://mynamespace#pred1> \"test\" }")) + .param("query", "INSERT \n DATA\n {\n <http://mynamespace/ProductType1> <http://mynamespace#pred1> \"test\" }")) .andExpect(status().isOk()); ValueFactory vf = repository.getValueFactory();
