// TEMPORARY
private boolean checkResultsByModel(
Query query, Model expectedModel, ResultSetRewindable results) {
// Fudge - can't cope with ordered results properly. The output writer for ResultSets does nto
// add rs:index.
results.reset();
Model actualModel = ResultSetFormatter.toModel(results);
// Tidy the models.
// Very regretable.
expectedModel.removeAll(null, RDF.type, ResultSetGraphVocab.ResultSet);
expectedModel.removeAll(null, RDF.type, ResultSetGraphVocab.ResultSolution);
expectedModel.removeAll(null, RDF.type, ResultSetGraphVocab.ResultBinding);
expectedModel.removeAll(null, ResultSetGraphVocab.size, (RDFNode) null);
expectedModel.removeAll(null, ResultSetGraphVocab.index, (RDFNode) null);
actualModel.removeAll(null, RDF.type, ResultSetGraphVocab.ResultSet);
actualModel.removeAll(null, RDF.type, ResultSetGraphVocab.ResultSolution);
actualModel.removeAll(null, RDF.type, ResultSetGraphVocab.ResultBinding);
actualModel.removeAll(null, ResultSetGraphVocab.size, (RDFNode) null);
actualModel.removeAll(null, ResultSetGraphVocab.index, (RDFNode) null);
boolean b = expectedModel.isIsomorphicWith(actualModel);
if (!b) {
System.out.println("---- Expected");
expectedModel.write(System.out, "TTL");
System.out.println("---- Actual");
actualModel.write(System.out, "TTL");
System.out.println("----");
}
return b;
}
/**
* Remove a Resource from the specified model. If property is null, the entire resource will be
* removed. Otherwise only the specified property will be removed from the resource.
*
* @param path2db (location of the TDB store).
* @param uri (base URI of the resource):
* @param id (resource id).
* @param property (property of the resource). can be null.
*/
public static void removeResource(String path2db, String uri, String id, Property property) {
// TDB.setExecutionLogging(InfoLevel.INFO);
TDB.getContext().set(TDB.symLogExec, true);
rdf_model = TDBFactory.createModel(path2db);
if (property == null) {
rdf_model.removeAll(rdf_model.createResource(uri + id), null, null);
} else {
rdf_model.removeAll(rdf_model.createResource(uri + id), property, null);
}
}
private void verbModel(Model model, String verb) {
Model m = ModelFactory.createDefaultModel();
int testLimit = 1000;
StmtIterator stmtIt = model.listStatements();
int count = 0;
try {
while (stmtIt.hasNext()) {
count++;
m.add(stmtIt.nextStatement());
if (count % testLimit == 0 || !stmtIt.hasNext()) {
StringWriter sw = new StringWriter();
m.write(sw, "N-TRIPLE");
StringBuffer updateStringBuff = new StringBuffer();
String graphURI = graph.getGraphURI();
updateStringBuff.append(
verb + " DATA { " + ((graphURI != null) ? "GRAPH <" + graphURI + "> { " : ""));
updateStringBuff.append(sw);
updateStringBuff.append(((graphURI != null) ? " } " : "") + " }");
String updateString = updateStringBuff.toString();
// log.info(updateString);
graph.executeUpdate(updateString);
m.removeAll();
}
}
} finally {
stmtIt.close();
}
}
@Override
public void clear() {
Model graph = null;
GraphConnection graphConnection = null;
try {
graphConnection = openGraph();
graph = graphConnection.getGraph();
graph.enterCriticalSection(Lock.READ);
graph.removeAll();
// XXX AT: remove reification quadlets explicitly
RSIterator it = graph.listReifiedStatements();
List<ReifiedStatement> rss = new ArrayList<ReifiedStatement>();
while (it.hasNext()) {
rss.add(it.nextRS());
}
for (ReifiedStatement rs : rss) {
graph.removeReification(rs);
}
} finally {
if (graph != null) {
graph.leaveCriticalSection();
}
if (graphConnection != null) {
graphConnection.close();
}
}
}
public void redoInferred(String uri, Model m, boolean nonMon) throws DataException {
log.info("Running inferences on " + uri);
Data data = getData();
Model infData = data.getModel(uri + "-inferred");
if (nonMon) infData.removeAll(); // Truth maintenance grossly simplified
InfModel inf = ModelFactory.createInfModel(reasoner, m);
infData.add(inf.getDeductionsModel());
log.info("Inferencing done");
}
/** @param value the value to set */
public void setValue(String value) {
this.value = value;
if (this.model != null && this.checksumNode != null) {
// delete any previous value
Property p =
model.getProperty(SpdxRdfConstants.SPDX_NAMESPACE, SpdxRdfConstants.PROP_CHECKSUM_VALUE);
model.removeAll(checksumResource, p, null);
// add the property
p =
model.createProperty(
SpdxRdfConstants.SPDX_NAMESPACE, SpdxRdfConstants.PROP_CHECKSUM_VALUE);
checksumResource.addProperty(p, value);
}
}
public boolean deleteAll(String uri) {
try {
log.info("Deleting model: " + uri + " " + reasoner);
Data data = getData();
Model m = data.getModel(uri);
m.removeAll();
if (reasoner != null) redoInferred(uri, m, true);
m.close();
data.close();
return true;
} catch (DataException e) {
e.printStackTrace();
return false;
}
}
/**
* @param algorithm the algorithm to set
* @throws InvalidSPDXAnalysisException
*/
public void setAlgorithm(String algorithm) throws InvalidSPDXAnalysisException {
this.algorithm = algorithm;
if (this.model != null && this.checksumNode != null) {
Resource algResource = algorithmStringToResource(algorithm, this.model);
// delete any previous algorithm
Property p =
model.getProperty(
SpdxRdfConstants.SPDX_NAMESPACE, SpdxRdfConstants.PROP_CHECKSUM_ALGORITHM);
model.removeAll(checksumResource, p, null);
// add the property
p =
model.createProperty(
SpdxRdfConstants.SPDX_NAMESPACE, SpdxRdfConstants.PROP_CHECKSUM_ALGORITHM);
checksumResource.addProperty(p, algResource);
}
}
public void run() {
try {
isSynchronizing = true;
while (removalModel.size() > 0 || additionModel.size() > 0) {
Model tempModel = ModelFactory.createDefaultModel();
removalModel.enterCriticalSection(Lock.WRITE);
try {
tempModel.add(removalModel);
removalModel.removeAll();
} finally {
removalModel.leaveCriticalSection();
}
pelletModel.enterCriticalSection(Lock.WRITE);
try {
pelletModel.remove(tempModel);
} finally {
pelletModel.leaveCriticalSection();
}
tempModel.removeAll();
additionModel.enterCriticalSection(Lock.WRITE);
try {
tempModel.add(additionModel);
additionModel.removeAll();
} finally {
additionModel.leaveCriticalSection();
}
pelletModel.enterCriticalSection(Lock.WRITE);
try {
pelletModel.add(tempModel);
} finally {
pelletModel.leaveCriticalSection();
}
tempModel = null;
getInferences();
}
} finally {
isSynchronizing = false;
}
}
/**
* Remove all data (triples) from the specified TDB store.
*
* @param path2db (location of the TDB store).
*/
public static void removeData(String path2db) {
// TDB.setExecutionLogging(InfoLevel.INFO);
TDB.getContext().set(TDB.symLogExec, true);
rdf_model = TDBFactory.createModel(path2db);
rdf_model.removeAll();
}
@Override
public void clear() {
model.removeAll();
}