litvinovg/vitro
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions

VIVO-773 Update the JENA libraries and adjust to the changes

Browse source 
Replace the JAR files with more current ones.
Add a one-line change to BaseInfGraph (from the Jena source), so it will work with Pellet 2.3.1
Adjust all implementations of Graph to include new methods and remove old ones.
Add annotations and generics to reduce compiler warnings.
Remove all dependencies on RDB, which is no longer supported.
   This requires considerable refactoring of JenaIngestController, RDFUploadController, listModels.jsp
Refactor the ModelMaker uses
   Remove VitroJenaModelMaker,
   Revise VitroInterceptingModelMaker to be configurable for Config or Content models
Add debug logging code to ModelChangeImpl ChangeSetImpl, RDFServiceJena.
Add TDB support: RDFServiceFactoryTDB, RDFServiceTDB
   Refactor RDFServiceJena and RDFServiceSDB so much of the code can be reused by RDFServiceTDB
Accomodate two RDFService instances - one for Configuration models and one for Content models.
   Changes to RDFServiceUtils, RDFServiceSetup
   Configuration models use TDB directory in Vitro home directory
Handle bulk updating:
   Jena has deprecated bulk operations, and their models classes no longer use the bulk updaters
   Create a VitroModelFactory to use instead of the ModelFactory, when bulk updating is required.
   Create adapter classes: BulkUpdatingModel, BulkUpdatingOntModel, AbstractModelDecorator
Make the configuration model setup algorithms uniform
   Combine ApplicationModelSetup and UserModelSetup into ConfigurationModelsSetup
This commit is contained in:
Jim Blake 2014-06-01 18:23:21 -04:00
parent 03c87f49a4
commit 3a2930cdc6
81 changed files with 6293 additions and 1628 deletions
Download patch file Download diff file Expand all files Collapse all files

544
webapp/src/com/hp/hpl/jena/reasoner/BaseInfGraph.java Normal file
View file

@ -0,0 +1,544 @@
/*
* 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 com.hp.hpl.jena.reasoner;
import com.hp.hpl.jena.graph.*;
import com.hp.hpl.jena.graph.compose.MultiUnion;
import com.hp.hpl.jena.graph.impl.*;
import com.hp.hpl.jena.shared.*;
import com.hp.hpl.jena.util.iterator.*;
import java.util.Iterator;
/**
* A base level implementation of the InfGraph interface.
*/
public abstract class BaseInfGraph extends GraphBase implements InfGraph {
/** The Reasoner instance which performs all inferences and Tbox lookups */
protected Reasoner reasoner;
/** The graph of raw data which is being reasoned over */
protected FGraph fdata;
/** Flag, if set to true then derivations are recorded */
protected boolean recordDerivations;
/** Flag to record if the preparation call has been made and so the graph is ready for queries */
protected volatile boolean isPrepared = false;
/** version count */
protected volatile int version = 0;
/**
Inference graphs share the prefix-mapping of their underlying raw graph.
@see com.hp.hpl.jena.graph.Graph#getPrefixMapping()
*/
@Override
public PrefixMapping getPrefixMapping()
{ return getRawGraph().getPrefixMapping(); }
/**
* Constructor
* @param data the raw data file to be augmented with entailments
* @param reasoner the engine, with associated tbox data, whose find interface
* can be used to extract all entailments from the data.
*/
public BaseInfGraph(Graph data, Reasoner reasoner) {
super( );
this.fdata = new FGraph( data );
this.reasoner = reasoner;
}
/**
Answer the InfCapabilities of this InfGraph.
*/
@Override
public Capabilities getCapabilities() {
if (capabilities == null) {
return getReasoner().getGraphCapabilities();
} else {
return capabilities;
}
}
/**
An InfCapabilities notes that size may not be accurate, and some
triples may be irremovable.
TODO accomodate the properties of the base graph, too.
*/
public static class InfCapabilities extends AllCapabilities
{
@Override
public boolean sizeAccurate() { return false; }
@Override
public boolean deleteAllowed( boolean every ) { return !every; }
@Override
public boolean iteratorRemoveAllowed() { return false; }
@Override
public boolean findContractSafe() { return false; }
}
/**
An InfCapabilities notes that size may not be accurate, and some
triples may be irremovable.
TODO accomodate the properties of the base graph, too.
*/
public static class InfFindSafeCapabilities extends InfCapabilities
{
@Override
public boolean findContractSafe() { return true; }
}
/**
@deprecated Bulk update operations are going to be removed.
@see GraphUtil for convenience helpers.
*/
@Override
@Deprecated
public BulkUpdateHandler getBulkUpdateHandler()
{
if (bulkHandler == null) bulkHandler = new InfBulkUpdateHandler( this );
return bulkHandler;
}
/**
InfBulkUpdateHandler - a bulk update handler specialised for inference
graphs by code for <code>removeAll()</code>.
*/
static class InfBulkUpdateHandler extends SimpleBulkUpdateHandler
{
public InfBulkUpdateHandler( BaseInfGraph graph )
{ super(graph); }
@Override
@Deprecated
public void remove( Node s, Node p, Node o )
{
BaseInfGraph g = (BaseInfGraph) graph;
g.getRawGraph().remove( s, p, o );
g.discardState();
g.rebind();
manager.notifyEvent( graph, GraphEvents.remove( s, p, o ) );
}
@Override
@Deprecated
public void removeAll()
{
BaseInfGraph g = (BaseInfGraph) graph;
g.getRawGraph().clear();
g.discardState();
g.rebind();
g.getEventManager().notifyEvent( g, GraphEvents.removeAll );
}
}
@Override
public void remove( Node s, Node p, Node o )
{
getRawGraph().remove( s, p, o );
discardState();
rebind();
getEventManager().notifyEvent( this, GraphEvents.remove( s, p, o ) );
}
@Override
public void clear()
{
getRawGraph().clear() ;
discardState();
rebind();
getEventManager().notifyEvent( this, GraphEvents.removeAll );
}
@Override
public TransactionHandler getTransactionHandler()
{ return new InfTransactionHandler( this ); }
public static class InfTransactionHandler
extends TransactionHandlerBase implements TransactionHandler
{
protected final BaseInfGraph base;
public InfTransactionHandler( BaseInfGraph base )
{ this.base = base; }
@Override
public boolean transactionsSupported()
{ return getBaseHandler().transactionsSupported(); }
protected TransactionHandler getBaseHandler()
{ return base.getRawGraph().getTransactionHandler(); }
@Override
public void begin()
{ getBaseHandler().begin(); }
@Override
public void abort()
{ getBaseHandler().abort();
base.rebind(); }
@Override
public void commit()
{ getBaseHandler().commit(); }
}
/**
discard any state that depends on the content of fdata, because
it's just been majorly trashed, solid gone.
*/
protected void discardState()
{}
/**
* Return the raw RDF data Graph being processed (i.e. the argument
* to the Reasonder.bind call that created this InfGraph).
*/
@Override
public Graph getRawGraph() {
return fdata.getGraph();
}
/**
* Return the Reasoner which is being used to answer queries to this graph.
*/
@Override
public Reasoner getReasoner() {
return reasoner;
}
/**
* Replace the underlying data graph for this inference graph and start any
* inferences over again. This is primarily using in setting up ontology imports
* processing to allow an imports multiunion graph to be inserted between the
* inference graph and the raw data, before processing.
* @param data the new raw data graph
*/
@Override
public synchronized void rebind(Graph data) {
fdata = new FGraph(data);
isPrepared = false;
}
/**
* Cause the inference graph to reconsult the underlying graph to take
* into account changes. Normally changes are made through the InfGraph's add and
* remove calls are will be handled appropriately. However, in some cases changes
* are made "behind the InfGraph's back" and this forces a full reconsult of
* the changed data.
*/
@Override
public synchronized void rebind() {
version++;
isPrepared = false;
}
/**
* Reset any internal caches. Some systems, such as the tabled backchainer,
* retain information after each query. A reset will wipe this information preventing
* unbounded memory use at the expense of more expensive future queries. A reset
* does not cause the raw data to be reconsulted and so is less expensive than a rebind.
*/
@Override
public void reset() {
version++;
}
/**
* Perform any initial processing and caching. This call is optional. Most
* engines either have negligable set up work or will perform an implicit
* "prepare" if necessary. The call is provided for those occasions where
* substantial preparation work is possible (e.g. running a forward chaining
* rule system) and where an application might wish greater control over when
* this prepration is done.
*/
@Override
public synchronized void prepare() {
// Default is to do no preparation
isPrepared = true;
}
/**
* Returns a derivations graph. The rule reasoners typically create a
* graph containing those triples added to the base graph due to rule firings.
* In some applications it can useful to be able to access those deductions
* directly, without seeing the raw data which triggered them. In particular,
* this allows the forward rules to be used as if they were rewrite transformation
* rules.
* @return the deductions graph, if relevant for this class of inference
* engine or null if not.
*/
@Override
public Graph getDeductionsGraph() {
return null;
}
/**
* Test a global boolean property of the graph. This might included
* properties like consistency, OWLSyntacticValidity etc.
* It remains to be seen what level of generality is needed here. We could
* replace this by a small number of specific tests for common concepts.
* @param property the URI of the property to be tested
* @return a Node giving the value of the global property, this may
* be a boolean literal, some other literal value (e.g. a size).
*/
@Override
public Node getGlobalProperty(Node property) {
throw new ReasonerException("Global property not implemented: " + property);
}
/**
* A convenience version of getGlobalProperty which can only return
* a boolean result.
*/
@Override
public boolean testGlobalProperty(Node property) {
Node resultNode = getGlobalProperty(property);
if (resultNode.isLiteral()) {
Object result = resultNode.getLiteralValue();
if (result instanceof Boolean) {
return ((Boolean)result).booleanValue();
}
}
throw new ReasonerException("Global property test returned non-boolean value" +
"\nTest was: " + property +
"\nResult was: " + resultNode);
}
/**
* Test the consistency of the bound data. This normally tests
* the validity of the bound instance data against the bound
* schema data.
* @return a ValidityReport structure
*/
@Override
public ValidityReport validate() {
checkOpen();
return new StandardValidityReport();
}
/**
* An extension of the Graph.find interface which allows the caller to
* encode complex expressions in RDF and then refer to those expressions
* within the query triple. For example, one might encode a class expression
* and then ask if there are any instances of this class expression in the
* InfGraph.
* @param subject the subject Node of the query triple, may be a Node in
* the graph or a node in the parameter micro-graph or null
* @param property the property to be retrieved or null
* @param object the object Node of the query triple, may be a Node in
* the graph or a node in the parameter micro-graph.
* @param param a small graph encoding an expression which the subject and/or
* object nodes refer.
*/
@Override
public ExtendedIterator<Triple> find(Node subject, Node property, Node object, Graph param) {
return cloneWithPremises(param).find(subject, property, object);
}
/**
* Returns an iterator over Triples.
*
* <p>This code used to have the .filterKeep component uncommented. We
* think this is because of earlier history, before .matches on a literal node
* was implemented as sameValueAs rather than equals. If it turns out that
* the filter is needed, it can be commented back in, AND a corresponding
* filter added to find(Node x 3) -- and test cases, of course.
*/
@Override
public ExtendedIterator<Triple> graphBaseFind(TripleMatch m) {
return graphBaseFind(m.getMatchSubject(), m.getMatchPredicate(), m.getMatchObject())
// .filterKeep(new TripleMatchFilter(m.asTriple()))
;
}
/**
* Returns an iterator over Triples.
* This implementation assumes that the underlying findWithContinuation
* will have also consulted the raw data.
*/
@Override
public ExtendedIterator<Triple> graphBaseFind(Node subject, Node property, Node object) {
return findWithContinuation(new TriplePattern(subject, property, object), fdata);
}
/**
* Extended find interface used in situations where the implementator
* may or may not be able to answer the complete query. It will
* attempt to answer the pattern but if its answers are not known
* to be complete then it will also pass the request on to the nested
* Finder to append more results.
* @param pattern a TriplePattern to be matched against the data
* @param continuation either a Finder or a normal Graph which
* will be asked for additional match results if the implementor
* may not have completely satisfied the query.
*/
abstract public ExtendedIterator<Triple> findWithContinuation(TriplePattern pattern, Finder continuation);
/**
* Basic pattern lookup interface.
* This implementation assumes that the underlying findWithContinuation
* will have also consulted the raw data.
* @param pattern a TriplePattern to be matched against the data
* @return a ExtendedIterator over all Triples in the data set
* that match the pattern
*/
public ExtendedIterator<Triple> find(TriplePattern pattern) {
checkOpen();
return findWithContinuation(pattern, fdata);
}
/**
* Switch on/off drivation logging
*/
@Override
public void setDerivationLogging(boolean logOn) {
recordDerivations = logOn;
}
/**
* Return the derivation of the given triple (which is the result of
* some previous find operation).
* Not all reasoneers will support derivations.
* @return an iterator over Derivation records or null if there is no derivation information
* available for this triple.
*/
@Override
public Iterator<Derivation> getDerivation(Triple triple) {
return null;
}
/**
* Return the number of triples in the just the base graph
*/
@Override
public int graphBaseSize() {
checkOpen();
return fdata.getGraph().size();
}
/**
Answer true iff this graph is empty. [Used to be in QueryHandler, but moved in
here because it's a more primitive operation.]
*/
@Override
public boolean isEmpty() {
return fdata.getGraph().isEmpty();
}
/**
* Free all resources, any further use of this Graph is an error.
*/
@Override
public void close() {
if (!closed) {
fdata.getGraph().close();
fdata = null;
super.close();
}
}
/**
* Return a version stamp for this graph which can be
* used to fast-fail concurrent modification exceptions.
*/
public int getVersion() {
return version;
}
/**
* Add one triple to the data graph, run any rules triggered by
* the new data item, recursively adding any generated triples.
*/
@Override
public synchronized void performAdd(Triple t) {
version++;
this.requirePrepared();
fdata.getGraph().add(t);
}
/**
* Removes the triple t (if possible) from the set belonging to this graph.
*/
@Override
public void performDelete(Triple t) {
version++;
this.requirePrepared();
fdata.getGraph().delete(t);
}
/**
* Return the schema graph, if any, bound into this inference graph.
*/
public abstract Graph getSchemaGraph();
/**
* Return a new inference graph which is a clone of the current graph
* together with an additional set of data premises. The default
* implementation loses ALL partial deductions so far. Some subclasses
* may be able to a more efficient job.
*/
public InfGraph cloneWithPremises(Graph premises) {
MultiUnion union = new MultiUnion();
Graph raw = getRawGraph();
union.addGraph( raw );
union.setBaseGraph( raw );
union.addGraph( premises );
Graph schema = getSchemaGraph();
if (schema != null) {
if (schema instanceof BaseInfGraph) {
BaseInfGraph ischema = (BaseInfGraph)schema;
Graph sschema = ischema.getSchemaGraph();
if (sschema != null) union.addGraph( sschema );
Graph rschema = ischema.getRawGraph();
if (rschema != null) union.addGraph( rschema );
}
}
return getReasoner().bind(union);
}
/**
Answer true iff this graph has been through the <code>prepare()</code> step.
For testing purposes.
* @return Whether the graph is prepared
*/
public synchronized boolean isPrepared()
{ return isPrepared; }
/**
* Reset prepared state to false
*/
protected synchronized void setPreparedState(boolean state) {
this.isPrepared = state;
}
/**
* Checks whether the graph is prepared and calls {@link #prepare()} if it is not
*/
protected synchronized void requirePrepared() {
if (!this.isPrepared) this.prepare();
}
}