private static void extractList(List<String> output, Resource head) {
if (head.hasProperty(RDF.first))
output.add(head.getProperty(RDF.first).getObject().asLiteral().getString());
if (head.hasProperty(RDF.rest))
extractList(output, head.getProperty(RDF.rest).getObject().asResource());
}
public static Offering convertOffering(Resource resource, Float price) {
Offering offering = new Offering();
offering.setId(resource.getLocalName());
if (resource.hasProperty(label)) {
offering.setName(resource.getProperty(label).getString());
} else {
offering.setName(resource.getLocalName());
}
if (resource.hasProperty(comment)) {
offering.setDescription(resource.getProperty(comment).getString());
}
// get included services
StmtIterator iter = resource.listProperties(includes);
// System.out.println(iter.toList().size());
while (iter.hasNext()) {
Resource service = iter.next().getResource();
offering = addFeatures(service, offering);
}
// get offering price
offering = getOfferingPrice(price, offering);
return offering;
}
private static QualitativeFeature convertQualitativeFeature(Resource r, String attributeType) {
QualitativeFeature qf = new QualitativeFeature();
qf.setType(QUAL_FEATURE.get(attributeType));
if (r.hasProperty(comment)) qf.setDescription(r.getProperty(comment).getString());
if (r.hasProperty(name)) qf.setName(r.getProperty(name).getString());
return qf;
}
public static String getVocabularyTitle(Model vocabulary, String uri) {
Resource nsResource = vocabulary.createResource(uri);
if (nsResource.hasProperty(DCTerms.title)) {
return nsResource.getProperty(DCTerms.title).getString();
} else if (nsResource.hasProperty(DC.title)) {
return nsResource.getProperty(DC.title).getString();
} else if (nsResource.hasProperty(RDFS.label))
return nsResource.getProperty(RDFS.label).getString();
return null;
}
private static QuantitativeFeature convertQuantitativeFeature(Resource r, String attributeType) {
QuantitativeFeature qf = new QuantitativeFeature();
qf.setName(r.getLocalName());
qf.setType(QUANT_FEATURE.get(attributeType));
if (r.hasProperty(comment)) qf.setDescription(r.getProperty(comment).getString());
if (r.hasProperty(hasValue)) qf.setValueFloat(r.getProperty(hasValue).getFloat());
if (r.hasProperty(hasUnitOfMeasurement))
qf.setUnitOfMeasurement(
UNIT_OF_MEASUREMENT.get(r.getProperty(hasUnitOfMeasurement).getString()));
return qf;
}
public static URI objectUriOfPropertyOfResource(Property property, Resource resource) {
try {
return new URI(resource.getProperty(property).getObject().asResource().getURI());
} catch (URISyntaxException e) {
throw new RuntimeException(e);
}
}
DeviceData(Resource device) {
this.device = device;
if (device.hasProperty(DeliSchema.manufacturedBy)) {
if (device.getProperty(DeliSchema.manufacturedBy).getResource().hasProperty(RDFS.label)) {
this.manufacturerName =
device
.getProperty(DeliSchema.manufacturedBy)
.getResource()
.getProperty(RDFS.label)
.getString();
}
}
if (device.hasProperty(DeliSchema.deviceName)) {
this.deviceName = device.getProperty(DeliSchema.deviceName).getString();
}
}
/**
* Returns the identifier of an LSRN-typed Resource
*
* @param lsrnNode
* @return the identifier
*/
public static String getID(Resource lsrnNode) {
Set<String> namespaces = new HashSet<String>();
for (Iterator<Resource> types = RdfUtils.getTypes(lsrnNode); types.hasNext(); ) {
Resource type = types.next();
if (type.isURIResource()) {
String ns = getNamespaceFromLSRNTypeURI(type.getURI());
if (ns != null) namespaces.add(ns);
}
}
Iterator<Resource> ids =
RdfUtils.getPropertyValues(lsrnNode, SIO.has_identifier, null)
.andThen(RdfUtils.getPropertyValues(lsrnNode, SIO.has_attribute, null));
while (ids.hasNext()) {
Resource identifier = ids.next();
for (Iterator<Resource> types = RdfUtils.getTypes(identifier); types.hasNext(); ) {
Resource type = types.next();
if (type.isURIResource()) {
String ns = getNamespaceFromLSRNIdentifierTypeURI(type.getURI());
if (ns != null && namespaces.contains(ns)) {
Statement s = identifier.getProperty(SIO.has_value);
if (s != null) {
return s.getString();
}
}
}
}
}
return null;
}
public MappedResource getIndexResource() {
if (!config.hasProperty(CONF.indexResource)) {
return null;
}
return getMappedResourceFromDatasetURI(
config.getProperty(CONF.indexResource).getResource().getURI());
}
@Override
public void processInput(Resource input, Resource output) {
Printing.print(input.getModel());
// Extract the link to the JSON specification
Literal jsonSpecificationURL =
input.getProperty(Vocabulary.hasJSONExperimentSpecificationURL).getLiteral();
JSONSpecification jsonSpec = new JSONSpecification(getURL(jsonSpecificationURL));
String jsonSpecID = jsonSpec.getSpecID();
// Create output model
Model outputModel = ModelFactory.createDefaultModel();
// Create the UnpostedScenario
ResourceURI resourceURI = new ResourceURI();
Resource unpostedScenario =
outputModel.createResource(
resourceURI.getURI("unpublishedScenario", jsonSpecID).toASCIIString(),
Vocabulary.UnpostedScenario);
unpostedScenario.addProperty(Vocabulary.hasScenarioLayer, input);
unpostedScenario.addLiteral(Vocabulary.hasJSONExperimentSpecificationURL, jsonSpecificationURL);
// Merge our temporary output model
output.getModel().add(outputModel);
// Set output scenario layer to reference parent scenario
output.addProperty(Vocabulary.isScenarioLayerOf, unpostedScenario);
Printing.print(output.getModel());
}
/** @see com.hp.hpl.jena.rdf.model.Resource#getProperty(com.hp.hpl.jena.rdf.model.Property) */
public Statement getProperty(Property p) {
synchronized (model) {
Statement wrappedResult = wrapped.getProperty(p);
if (wrappedResult == null) {
return null;
}
return new ThreadSafeStatement(model, wrappedResult);
}
}
protected Set<ValueFactory> getValueFactory(RDFNode valueNode, OntModel displayOntModel) {
// maybe use jenabean or owl2java for this?
if (valueNode.isResource()) {
Resource res = (Resource) valueNode.as(Resource.class);
Statement stmt = res.getProperty(DisplayVocabulary.JAVA_CLASS_NAME);
if (stmt == null || !stmt.getObject().isLiteral()) {
log.debug("Cannot build value factory: java class was " + stmt.getObject());
return Collections.emptySet();
}
String javaClassName = ((Literal) stmt.getObject().as(Literal.class)).getLexicalForm();
if (javaClassName == null || javaClassName.length() == 0) {
log.debug("Cannot build value factory: no java class was set.");
return Collections.emptySet();
}
Class<?> clazz;
Object newObj;
try {
clazz = Class.forName(javaClassName);
} catch (ClassNotFoundException e) {
log.debug("Cannot build value factory: no class found for " + javaClassName);
return Collections.emptySet();
}
try {
newObj = clazz.newInstance();
} catch (Exception e) {
log.debug(
"Cannot build value factory: exception while creating object of java class "
+ javaClassName
+ " "
+ e.getMessage());
return Collections.emptySet();
}
if (newObj instanceof ValueFactory) {
ValueFactory valueFactory = (ValueFactory) newObj;
return Collections.singleton(valueFactory);
} else {
log.debug(
"Cannot build value factory: "
+ javaClassName
+ " does not implement "
+ ValueFactory.class.getName());
return Collections.emptySet();
}
} else {
log.debug("Cannot build value factory for " + valueNode);
return Collections.emptySet();
}
}
public static void main(String[] args) {
Model adapterModel =
OntologyModelUtil.loadModel("ontologies/docker.ttl", IMessageBus.SERIALIZATION_TURTLE);
Property propCommand =
adapterModel.getProperty(adapterModel.getNsPrefixURI("docker"), "command");
Model m = OntologyModelUtil.loadModel("test.ttl", IMessageBus.SERIALIZATION_TURTLE);
ResIterator rs = m.listResourcesWithProperty(propCommand);
while (rs.hasNext()) {
Resource r = rs.next();
Statement c = r.getProperty(propCommand);
Resource listHead = c.getObject().asResource();
LinkedList<String> output = new LinkedList<String>();
extractList(output, listHead);
for (String elem : output) {
System.out.println("elem: " + elem);
}
}
}
/**
* @see org.caboto.jena.db.Database#updateProperty(java.lang.String, java.lang.String,
* com.hp.hpl.jena.rdf.model.Property, com.hp.hpl.jena.rdf.model.RDFNode)
*/
public boolean updateProperty(String uri, String resourceUri, Property property, RDFNode value) {
try {
log.info("Updting property in model: " + uri + " " + reasoner);
Data data = getData();
Model m = data.getModel(uri);
if (!m.containsResource(ResourceFactory.createResource(resourceUri))) {
m.close();
data.close();
return false;
}
Resource resource = m.getResource(resourceUri);
if (resource.hasProperty(property)) {
resource.getProperty(property).changeObject(value);
} else {
resource.addProperty(property, value);
}
m.close();
data.close();
return true;
} catch (DataException e) {
e.printStackTrace();
return false;
}
}
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;
}
public String getWebApplicationBaseURI() {
return config.getProperty(CONF.webBase).getResource().getURI();
}
public String getProjectName() {
return config.getProperty(CONF.projectName).getString();
}
public String getProjectLink() {
return config.getProperty(CONF.projectHomepage).getResource().getURI();
}
@Test
public void testConversion() throws Exception {
status.put(DepositField.sourcePath.name(), "src/test/resources/paths/valid-bag");
status.put(DepositField.fileName.name(), "Test File");
status.put(
DepositField.extras.name(), "{\"accessionNumber\" : \"123456\", \"mediaId\" : \"789\"}");
when(stages.getStagedURI(any(URI.class)))
.thenAnswer(
new Answer<URI>() {
public URI answer(InvocationOnMock invocation) throws URISyntaxException {
Object[] args = invocation.getArguments();
URI uri = (URI) args[0];
String path = uri.toString();
int index = path.lastIndexOf("/paths");
path = path.substring(index + 6);
return new URI("tag:" + path);
}
});
job.run();
Model model = job.getReadOnlyModel();
Bag depositBag = model.getBag(job.getDepositPID().getURI());
assertEquals(depositBag.size(), 1);
Bag bagFolder = model.getBag((Resource) depositBag.iterator().next());
assertEquals(
"Bag folder label was not set",
"Test File",
bagFolder.getProperty(dprop(model, label)).getString());
assertEquals(
"Content model was not set",
CONTAINER.toString(),
bagFolder.getPropertyResourceValue(fprop(model, hasModel)).getURI());
Resource folder = (Resource) bagFolder.iterator().next();
assertEquals(
"Folder label was not set", folder.getProperty(dprop(model, label)).getString(), "test");
assertEquals(
"Content model was not set",
CONTAINER.toString(),
folder.getPropertyResourceValue(fprop(model, hasModel)).getURI());
Bag childrenBag = model.getBag(folder.getURI());
assertEquals(childrenBag.size(), 2);
// Put children into a map since we can't guarantee order from jena
Map<String, Resource> children = new HashMap<>(2);
NodeIterator childIt = childrenBag.iterator();
while (childIt.hasNext()) {
Resource file = (Resource) childIt.next();
children.put(file.getProperty(dprop(model, label)).getString(), file);
}
ArgumentCaptor<String> filePathCaptor = ArgumentCaptor.forClass(String.class);
verify(depositStatusFactory, times(2)).addManifest(anyString(), filePathCaptor.capture());
List<String> capturedFilePaths =
Arrays.asList("tag:/valid-bag/bagit.txt", "tag:/valid-bag/manifest-md5.txt");
assertEquals(capturedFilePaths, filePathCaptor.getAllValues());
Resource file = children.get("lorem.txt");
assertEquals(
"Content model was not set",
SIMPLE.toString(),
file.getPropertyResourceValue(fprop(model, hasModel)).getURI());
assertEquals(
"Checksum was not set",
"fa5c89f3c88b81bfd5e821b0316569af",
file.getProperty(dprop(model, md5sum)).getString());
assertEquals(
"File location not set",
"tag:/valid-bag/data/test/lorem.txt",
file.getProperty(dprop(model, stagingLocation)).getString());
Resource file2 = children.get("ipsum.txt");
assertEquals(
"Content model was not set",
SIMPLE.toString(),
file2.getPropertyResourceValue(fprop(model, hasModel)).getURI());
assertEquals(
"Checksum was not set",
"e78f5438b48b39bcbdea61b73679449d",
file2.getProperty(dprop(model, md5sum)).getString());
assertEquals(
"File location not set",
"tag:/valid-bag/data/test/ipsum.txt",
file2.getProperty(dprop(model, stagingLocation)).getString());
File modsFile =
new File(job.getDescriptionDir(), new PID(bagFolder.getURI()).getUUID() + ".xml");
assertTrue(modsFile.exists());
Set<String> cleanupSet = new HashSet<>();
StmtIterator it = depositBag.listProperties(dprop(model, cleanupLocation));
while (it.hasNext()) {
Statement stmt = it.nextStatement();
cleanupSet.add(stmt.getString());
}
assertEquals("Incorrect number of objects identified for cleanup", 3, cleanupSet.size());
assertTrue("Cleanup of bag not set", cleanupSet.contains("tag:/valid-bag/"));
assertTrue("Cleanup of manifest not set", cleanupSet.contains("tag:/valid-bag/bagit.txt"));
assertTrue(
"Cleanup of manifest not set", cleanupSet.contains("tag:/valid-bag/manifest-md5.txt"));
}
public String getDefaultLanguage() {
if (!config.hasProperty(CONF.defaultLanguage)) {
return null;
}
return config.getProperty(CONF.defaultLanguage).getString();
}
String getRelease() {
return device.getProperty(DeliSchema.release).getString();
}
String getProvider() {
return device.getProperty(DeliSchema.provider).getResource().getURI();
}
@Override
public Protocol fromJena(Model source, Resource res) throws IllegalArgumentException {
Protocol protocol = new Protocol();
try {
protocol.setResourceURL(new URL(res.getURI()));
} catch (MalformedURLException e) {
throw new IllegalArgumentException(String.format(msg_InvalidURI, "protocol", res.getURI()));
}
try {
protocol.setSearchable(res.getProperty(TOXBANK.ISSUMMARYSEARCHABLE).getBoolean());
} catch (Exception x) {
protocol.setSearchable(false);
}
try {
protocol.setVersion(res.getProperty(TOXBANK.HASVERSIONINFO).getInt());
} catch (Exception x) {
protocol.setVersion(0);
}
try {
protocol.setPublished(res.getProperty(TOXBANK.ISPUBLISHED).getBoolean());
} catch (Exception x) {
protocol.setPublished(null);
}
try {
protocol.setTimeModified(res.getProperty(DCTerms.modified).getLong());
} catch (Exception x) {
protocol.setTimeModified(null);
}
try {
protocol.setSubmissionDate(res.getProperty(DCTerms.dateSubmitted).getLong());
} catch (Exception x) {
protocol.setSubmissionDate(null);
}
if (res.getProperty(DCTerms.title) != null)
protocol.setTitle(res.getProperty(DCTerms.title).getString());
if (res.getProperty(TOXBANK.HASSTATUS) != null)
try {
protocol.setStatus(Protocol.STATUS.valueOf(res.getProperty(TOXBANK.HASSTATUS).getString()));
} catch (Exception x) {
protocol.setStatus(STATUS.RESEARCH);
}
if (res.getProperty(DCTerms.identifier) != null)
protocol.setIdentifier(res.getProperty(DCTerms.identifier).getString());
if (res.getProperty(TOXBANK.HASABSTRACT) != null)
protocol.setAbstract(res.getProperty(TOXBANK.HASABSTRACT).getString());
StmtIterator keywords = res.listProperties(TOXBANK.HASKEYWORD);
while (keywords.hasNext()) {
protocol.addKeyword(keywords.next().getString());
}
String uri = null;
StmtIterator authors = res.listProperties(TOXBANK.HASAUTHOR);
while (authors.hasNext()) {
Resource authorRes = authors.next().getResource();
User author = userIO.fromJena(source, authorRes);
protocol.addAuthor(author);
}
authors.close();
StmtIterator projects = res.listProperties(TOXBANK.HASPROJECT);
while (projects.hasNext()) {
Resource projectRes = projects.next().getResource();
Project project = projectIO.fromJena(source, projectRes);
protocol.addProject(project);
}
projects.close();
if (res.getProperty(TOXBANK.HASORGANISATION) != null) {
Organisation org =
organisationIO.fromJena(source, res.getProperty(TOXBANK.HASORGANISATION).getResource());
protocol.setOrganisation(org);
}
if (res.getProperty(TOXBANK.HASOWNER) != null)
try {
uri = res.getProperty(TOXBANK.HASOWNER).getResource().getURI();
User author = new User();
author.setResourceURL(new URL(uri));
protocol.setOwner(author);
} catch (MalformedURLException e) {
throw new IllegalArgumentException(String.format(msg_InvalidURI, "a protocol owner", uri));
}
if (res.getProperty(TOXBANK.HASDOCUMENT) != null)
try {
uri = res.getProperty(TOXBANK.HASDOCUMENT).getResource().getURI();
Document document = new Document(new URL(uri));
protocol.setDocument(document);
} catch (MalformedURLException e) {
throw new IllegalArgumentException(String.format(msg_InvalidURI, "a document", uri));
}
if (res.getProperty(TOXBANK.HASTEMPLATE) != null)
try {
uri = res.getProperty(TOXBANK.HASTEMPLATE).getResource().getURI();
Template dataTemplate = new Template(new URL(uri));
protocol.setDataTemplate(dataTemplate);
} catch (MalformedURLException e) {
throw new IllegalArgumentException(String.format(msg_InvalidURI, "data template", uri));
}
if (res.getProperty(DCTerms.license) != null)
try {
protocol.setLicense(new URL(res.getProperty(DCTerms.license).getObject().toString()));
} catch (MalformedURLException e) {
throw new IllegalArgumentException(
String.format(
msg_InvalidURI, "a license", res.getProperty(DCTerms.license).getObject()));
}
return protocol;
}
private void addLabel(Resource blankNode, Resource queryNode, Model outputModel) {
final Statement labelStatement = queryNode.getProperty(RDFS.label);
if (labelStatement != null) {
outputModel.add(blankNode, RDFS.label, labelStatement.getObject());
}
}
