public void deduceLocation() {
Property loc = model.getModel().getProperty(uri, "hasLocation");
for (Resource human : humans) {
Statement ss1 = null;
String s = "";
Resource r = null;
StmtIterator locii = model.getModel().listStatements(human, loc, (RDFNode) null);
if (locii.hasNext()) {
ss1 = (Statement) locii.next();
System.out.println(
"initial statements:"
+ ss1.getSubject().getLocalName()
+ " "
+ ss1.getPredicate().getLocalName()
+ " "
+ ss1.getResource().getLocalName());
}
StmtIterator loci = infmodel.getDeductionsModel().listStatements(human, loc, (RDFNode) null);
if (loci.hasNext()) {
Statement ssl = (Statement) loci.next();
RDFNode obj = (RDFNode) ssl.getObject();
if (obj instanceof Resource) {
r = (Resource) obj;
s = r.getLocalName();
} else {
System.out.print("!!! Literal");
}
System.out.println(
"Inferred: user: "******" changed location to room "
+ s);
}
if (r != null) ss1.changeObject(r);
StmtIterator fi = model.getModel().listStatements(human, loc, (RDFNode) null);
while (fi.hasNext()) {
Statement ss = (Statement) fi.next();
System.out.println(
"After updating the ontology \n"
+ ss.getSubject().getLocalName()
+ " "
+ ss.getPredicate().getLocalName()
+ " "
+ ss.getResource().getLocalName());
}
}
}
public void deduceAuthorization() {
Property auth = model.getModel().getProperty(uri, "isAuthenticatedBy");
for (Resource human : humans) {
Resource r = null;
StmtIterator ii = model.getModel().listStatements(human, auth, (RDFNode) null);
if (ii.hasNext()) {
Statement ss1 = (Statement) ii.next();
System.out.println(
"initial statements:"
+ ss1.getSubject().getLocalName()
+ " "
+ ss1.getPredicate().getLocalName()
+ " "
+ ss1.getResource().getLocalName());
StmtIterator iii =
infmodel.getDeductionsModel().listStatements(human, auth, (RDFNode) null);
if (iii.hasNext()) {
Statement ss2 = (Statement) iii.next();
System.out.println(
"inferred: "
+ ss2.getSubject().getLocalName()
+ " "
+ ss2.getPredicate().getLocalName()
+ " "
+ ss2.getResource().getLocalName());
r = ss2.getResource();
}
if (r != null) ss1.changeObject(r);
StmtIterator fi = model.getModel().listStatements(human, auth, (RDFNode) null);
while (fi.hasNext()) {
Statement ss = (Statement) fi.next();
System.out.println(
"After updating the ontology \n"
+ ss.getSubject().getLocalName()
+ " "
+ ss.getPredicate().getLocalName()
+ " "
+ ss.getResource().getLocalName());
}
}
}
}
/**
* Deletes the given process element from the rnrm:isFlowingTo linked list without breaking the
* path. The element is also removed from the process.
*
* @param processElement
*/
public void deleteFromPath(Resource processElement) {
Model model = process.getModel();
List<Statement> incoming = process.getIncomingEdges(processElement);
List<Statement> outgoing = process.getOutgoingEdges(processElement);
if (incoming.size() > 1 || outgoing.size() > 1) {
throw new IllegalArgumentException(
"Error deleting element. Elements with more than 1 outgoing or incoming links cannot be deleted.");
}
Resource before = null;
Resource after = null;
Statement stmt = null;
if (incoming.size() > 0) {
stmt = incoming.get(0);
before = stmt.getSubject();
model.remove(stmt);
}
if (outgoing.size() > 0) {
stmt = outgoing.get(0);
after = stmt.getResource();
model.remove(stmt);
}
if (null != before && null != after) {
model.add(before, RNRM.isFlowingTo, after);
}
// now disassociate this element from the process
removeFromProcess(processElement);
}
@Override
public void processInput(Resource input, Resource output) {
final Model model = ModelFactory.createDefaultModel();
final List<Statement> tipURIs = input.listProperties(Vocab.has).toList();
final SublistIterator<Statement> tipsIterator =
new SublistIterator<Statement>(tipURIs, QUERY_CHUNK_SIZE);
while (tipsIterator.hasNext()) {
final List<String> ancestorQueryBlocks = new ArrayList<String>();
final List<String> parentQueryBlocks = new ArrayList<String>();
final List<Statement> tips = tipsIterator.next();
for (Statement statement : tips) {
final String tipURI =
statement.getResource().getProperty(DC.subject).getResource().getURI();
ancestorQueryBlocks.add(String.format(ancestorQueryBody, tipURI));
parentQueryBlocks.add(String.format(parentQueryBody, tipURI));
}
final String ancestorQuery =
String.format(ancestorQueryHead, StringUtils.join(ancestorQueryBlocks, " UNION "));
final String parentQuery =
String.format(parentQueryHead, StringUtils.join(parentQueryBlocks, ", "));
QueryEngineHTTP ancestorQE = new QueryEngineHTTP(endpoint, ancestorQuery);
QueryEngineHTTP parentQE = new QueryEngineHTTP(endpoint, parentQuery);
ancestorQE.execConstruct(model);
ancestorQE.close();
parentQE.execConstruct(model);
parentQE.close();
}
this.processNode(Vocab.TaxonomyRoot, model, output.getModel(), null, output);
output.getModel().setNsPrefix("cdao", "http://www.evolutionaryontology.org/cdao/1.0/cdao.owl#");
}
public Configuration(Model configurationModel) {
model = configurationModel;
StmtIterator it = model.listStatements(null, RDF.type, CONF.Configuration);
if (!it.hasNext()) {
throw new IllegalArgumentException("No conf:Configuration found in configuration model");
}
config = it.nextStatement().getSubject();
datasets = new ArrayList();
it = model.listStatements(config, CONF.dataset, (RDFNode) null);
while (it.hasNext()) {
datasets.add(new Dataset(it.nextStatement().getResource()));
}
labelProperties = new ArrayList();
it = model.listStatements(config, CONF.labelProperty, (RDFNode) null);
while (it.hasNext()) {
labelProperties.add(it.nextStatement().getObject().as(Property.class));
}
if (labelProperties.isEmpty()) {
labelProperties.add(RDFS.label);
labelProperties.add(DC.title);
labelProperties.add(model.createProperty("http://xmlns.com/foaf/0.1/name"));
}
commentProperties = new ArrayList();
it = model.listStatements(config, CONF.commentProperty, (RDFNode) null);
while (it.hasNext()) {
commentProperties.add(it.nextStatement().getObject().as(Property.class));
}
if (commentProperties.isEmpty()) {
commentProperties.add(RDFS.comment);
commentProperties.add(DC.description);
}
imageProperties = new ArrayList();
it = model.listStatements(config, CONF.imageProperty, (RDFNode) null);
while (it.hasNext()) {
imageProperties.add(it.nextStatement().getObject().as(Property.class));
}
if (imageProperties.isEmpty()) {
imageProperties.add(model.createProperty("http://xmlns.com/foaf/0.1/depiction"));
}
prefixes = new PrefixMappingImpl();
if (config.hasProperty(CONF.usePrefixesFrom)) {
it = config.listProperties(CONF.usePrefixesFrom);
while (it.hasNext()) {
Statement stmt = it.nextStatement();
prefixes.setNsPrefixes(FileManager.get().loadModel(stmt.getResource().getURI()));
}
} else {
prefixes.setNsPrefixes(model);
}
if (prefixes.getNsURIPrefix(CONF.NS) != null) {
prefixes.removeNsPrefix(prefixes.getNsURIPrefix(CONF.NS));
}
}
/**
* Inserts the given {@link Resource} into the rnrm:isFlowingTo path after the specified {@link
* Resource}
*
* @param toInsert Process element to insert
* @param after Process element to insert after
*/
public void insertAfter(Resource toInsert, Resource after) {
List<Statement> outgoing = process.getOutgoingEdges(after);
Model model = process.getModel();
if (outgoing.size() > 1) {
throw new IllegalArgumentException("Cannot insert after nodes with multiple outgoing links.");
}
model.add(after, RNRM.isFlowingTo, toInsert);
if (outgoing.size() > 0) {
Statement stmt = outgoing.get(0);
Resource next = stmt.getResource();
model.remove(stmt);
model.add(toInsert, RNRM.isFlowingTo, next);
}
}
public void print(PrintContext p) {
Variable asVar = getAs();
if (asVar != null) {
p.print("(");
}
Resource aggType = getResource(RDF.type);
String aggName = Aggregations.getName(aggType);
p.printKeyword(aggName);
p.print("(");
if (isDistinct()) {
p.print("DISTINCT ");
}
Statement exprS = getProperty(SP.expression);
if (exprS != null && exprS.getObject().isResource()) {
Resource r = exprS.getResource();
RDFNode expr = SPINFactory.asExpression(r);
if (expr instanceof Printable) {
((Printable) expr).print(p);
} else {
p.printURIResource(r);
}
} else {
p.print("*");
}
String separator = getString(SP.separator);
if (separator != null) {
p.print("; ");
p.printKeyword("SEPARATOR");
p.print("='" + StrUtils.escapeString(separator) + "'");
}
if (asVar != null) {
p.print(") ");
p.printKeyword("AS");
p.print(" ");
p.print(asVar.toString());
}
p.print(")");
}
/**
* Checks if spin:imports have been declared and adds them to a union model. Will also register
* any SPIN modules defined in those imports that haven't been loaded before.
*
* @param model the base Model to operate on
* @return either model or the union of model and its spin:imports @
*/
public Model getImportsModel(Model model) throws IOException {
Set<String> uris = new HashSet<String>();
StmtIterator it = model.listStatements(null, SPIN.imports, (RDFNode) null);
while (it.hasNext()) {
Statement s = it.nextStatement();
if (s.getObject().isURIResource()) {
uris.add(s.getResource().getURI());
}
}
if (uris.isEmpty()) {
return model;
} else {
Graph baseGraph = model.getGraph();
MultiUnion union = JenaUtil.createMultiUnion();
union.addGraph(baseGraph);
union.setBaseGraph(baseGraph);
boolean needsRegistration = false;
for (String uri : uris) {
Graph graph = getImportedGraph(uri);
if (graph != null) {
union.addGraph(graph);
if (!registeredURIs.contains(uri)) {
registeredURIs.add(uri);
needsRegistration = true;
}
}
}
// Ensure that SP, SPIN and SPL are present
ensureImported(union, SP.BASE_URI, SP.getModel());
ensureImported(union, SPL.BASE_URI, SPL.getModel());
ensureImported(union, SPIN.BASE_URI, SPIN.getModel());
Model unionModel = ModelFactory.createModelForGraph(union);
if (needsRegistration) {
SPINModuleRegistry.get().registerAll(unionModel, null);
}
return unionModel;
}
}
public int[] getSourceColumns(Resource resource) {
if (_model.contains(resource, Vertere.source_column)) {
Statement sourceColumn = _model.getProperty(resource, Vertere.source_column);
return new int[] {sourceColumn.getInt()};
} else if (_model.contains(resource, Vertere.source_columns)) {
Statement sourceColumns = _model.getProperty(resource, Vertere.source_columns);
Resource listResource = sourceColumns.getResource();
RDFList list = listResource.as(RDFList.class);
List<RDFNode> javalist = list.asJavaList();
int[] sourceColumnNumbers = new int[javalist.size()];
for (int i = 0; i < javalist.size(); i++) {
RDFNode node = javalist.get(i);
Literal value = node.asLiteral();
sourceColumnNumbers[i] = value.getInt();
}
return sourceColumnNumbers;
} else {
return new int[0];
}
}
public Organization getOrganization(String organizationUri) {
long startTime = System.currentTimeMillis();
Organization org = new Organization();
// ResIterator iter =
// ontModel.listSubjectsWithProperty(ontModel.getProperty(ORGID),organizationId);
Resource r = ontModel.getResource(organizationUri);
if (r != null) {
// Resource r = iter.nextResource();
org.setUri(organizationUri);
StmtIterator typeStmtIter = r.listProperties(ontModel.getProperty(TYPE));
Resource organizationalCollaboration = ontModel.getResource(ORGANIZATIONALCOLLABORATION);
while (typeStmtIter.hasNext()) {
Statement typeStmt = typeStmtIter.next();
if (typeStmt != null) {
String organizationClass = typeStmt.getResource().getURI();
if (organizationClass.equalsIgnoreCase(organizationalCollaboration.getURI()))
org.setOrganizationalCollaboration(true);
}
}
Statement id = r.getProperty(ontModel.getProperty(ORGID));
if (id != null) org.setId(id.getString());
Statement title = r.getProperty(ontModel.getProperty(TITLE));
if (title != null) org.setTitle(title.getString());
Statement preflabel = r.getProperty(ontModel.getProperty(PREFLABEL));
if (preflabel != null) org.setPrefLabel(preflabel.getString());
Statement purpose = r.getProperty(ontModel.getProperty(PURPOSE));
if (purpose != null) org.setPurpose(purpose.getString());
Statement description = r.getProperty(ontModel.getProperty(DESCRIPTION));
if (description != null) org.setDescription(description.getString());
Statement classification = r.getProperty(ontModel.getProperty(CLASSIFICATION));
if (classification != null) {
Resource classificationObj = classification.getObject().asResource();
Statement preflabelClassification =
classificationObj.getProperty(ontModel.getProperty(PREFLABEL));
org.setClassification(preflabelClassification.getString());
}
// depiction
Statement depiction = r.getProperty(ontModel.getProperty(DEPICTION));
if (depiction != null) {
Statement depicts = depiction.getProperty(ontModel.getProperty(DEPICTS));
if (depicts != null) {
Resource imgRes = depicts.getResource();
if (imgRes != null) org.setDepicts(depicts.getResource().getURI());
}
}
// memberOrganizations
StmtIterator memberOrgIter = r.listProperties(ontModel.getProperty(HASMEMBERORGANIZATION));
ArrayList<String> hasMemberOrganization = new ArrayList<String>();
while (memberOrgIter.hasNext()) {
Statement stmtMembOrg = memberOrgIter.next();
Resource memberOrgRes = stmtMembOrg.getResource();
if (memberOrgRes != null) {
// Statement memberOrgStmt = memberOrgRes.getProperty(ontModel.getProperty(ORGID));
// if (memberOrgStmt!=null)
// hasMemberOrganization.add(memberOrgStmt.getString());
hasMemberOrganization.add(memberOrgRes.getURI());
}
}
org.setHasMemberOrganization(hasMemberOrganization);
// hasProject
StmtIterator projectOrgIter = r.listProperties(ontModel.getProperty(HASPROJECT));
ArrayList<String> hasProject = new ArrayList<String>();
while (projectOrgIter.hasNext()) {
Statement stmtProjOrg = projectOrgIter.next();
Resource projRes = stmtProjOrg.getResource();
if (projRes != null) {
hasProject.add(projRes.getURI());
}
}
org.setHasProject(hasProject);
// hasProduct
StmtIterator productOrgIter = r.listProperties(ontModel.getProperty(HASPRODUCT));
ArrayList<String> hasProduct = new ArrayList<String>();
while (productOrgIter.hasNext()) {
Statement stmtProdOrg = productOrgIter.next();
Resource prodRes = stmtProdOrg.getResource();
if (prodRes != null) {
hasProduct.add(prodRes.getURI());
}
}
org.setHasProduct(hasProduct);
// hasMember
StmtIterator hasMemberIter = r.listProperties(ontModel.getProperty(HASMEMBER));
ArrayList<String> hasMember = new ArrayList<String>();
while (hasMemberIter.hasNext()) {
Statement stmtHasMember = hasMemberIter.next();
Resource personRes = stmtHasMember.getResource();
if (personRes != null) {
// Statement personIdStmt = personRes.getProperty(ontModel.getProperty(PERSONID));
// if (personIdStmt!=null)
// hasMember.add(personIdStmt.getString());
hasMember.add(personRes.getURI());
}
}
org.setHasMember(hasMember);
// organizationPosition
StmtIterator orgPositionIter = r.listProperties(ontModel.getProperty(ORGPOSITION));
ArrayList<String> position = new ArrayList<String>();
while (orgPositionIter.hasNext()) {
Statement stmtOrgPosition = orgPositionIter.next();
Resource positionRes = stmtOrgPosition.getResource();
if (positionRes != null) {
position.add(positionRes.getURI());
}
}
org.setPosition(position);
// organizationRole
StmtIterator orgRoleIter = r.listProperties(ontModel.getProperty(ORGROLE));
ArrayList<String> role = new ArrayList<String>();
while (orgRoleIter.hasNext()) {
Statement stmtOrgRole = orgRoleIter.next();
Resource roleRes = stmtOrgRole.getResource();
if (roleRes != null) {
role.add(roleRes.getURI());
}
}
org.setRole(role);
// membership
StmtIterator membershipIter = r.listProperties(ontModel.getProperty(MEMBERSHIP));
ArrayList<String> membership = new ArrayList<String>();
while (membershipIter.hasNext()) {
Statement stmtMembership = membershipIter.next();
Resource membershipRes = stmtMembership.getResource();
if (membershipRes != null) {
membership.add(membershipRes.getURI());
}
}
org.setMembership(membership);
long stopTime = System.currentTimeMillis();
long elapsedTime = stopTime - startTime;
LOGGER.debug("- Load the organization, elapsed time (ms)..: {}", elapsedTime);
}
return org;
}