/** Load local dataset into TDB */
private void TDBloading(String fileDump) {
logger.info("TDB creation");
// create tdb from .nt local file
FileManager fm = FileManager.get();
fm.addLocatorClassLoader(RDFTripleExtractor.class.getClassLoader());
InputStream in = fm.open(fileDump);
Location location = new Location(tdbDirectory);
// load some initial data
try {
TDBLoader.load(
TDBInternal.getBaseDatasetGraphTDB(TDBFactory.createDatasetGraph(location)), in, true);
} catch (Exception e) {
logger.error("TDB loading error: " + e.getMessage());
}
logger.info("TDB loading");
// create model from tdb
Dataset dataset = TDBFactory.createDataset(tdbDirectory);
// assume we want the default model, or we could get a named model here
dataset.begin(ReadWrite.READ);
model = dataset.getDefaultModel();
dataset.end();
}
/** Initializes the servlet. */
@Override
public void init(ServletConfig config) throws ServletException {
super.init(config);
// It seems that if the servlet fails to initialize the first time,
// init can be called again (it has been observed in Tomcat log files
// but not explained).
if (initAttempted) {
// This happens - the query and update servlets share this class
// log.info("Re-initialization of servlet attempted") ;
return;
}
initAttempted = true;
servletConfig = config;
// Modify the (Jena) global filemanager to include loading by servlet context
FileManager fileManager = FileManager.get();
if (config != null) {
servletContext = config.getServletContext();
fileManager.addLocator(new LocatorServletContext(servletContext));
}
printName = config.getServletName();
String configURI = config.getInitParameter(Joseki.configurationFileProperty);
servletEnv();
try {
Dispatcher.initServiceRegistry(fileManager, configURI);
} catch (ConfigurationErrorException confEx) {
throw new ServletException("Joseki configuration error", confEx);
}
}
/* loads sample data from a file */
protected Model loadInstanceData(String dataFile) {
FileManager fileManager = new FileManager();
fileManager.addLocatorClassLoader(this.getClass().getClassLoader());
fileManager.addLocatorFile();
Model inputModel = fileManager.loadModel(dataFile);
return inputModel;
}
/**
* Run the consistency check, returning a ValidityReport.
*
* @param rf The factory for the reasoner to test
*/
public ValidityReport testResults() {
Model t = FileManager.get().loadModel(BASE_DIR + tbox);
Model a = FileManager.get().loadModel(BASE_DIR + abox);
// Work around non-deterministic bug in bindSchema
// Reasoner r = rf.create(null).bindSchema(t);
Reasoner r = rf.create(null);
a.add(t);
InfModel im = ModelFactory.createInfModel(r, a);
return im.validate();
}
public static Model readModel(String fileNameOrUri) {
long startTime = System.currentTimeMillis();
Model model = ModelFactory.createDefaultModel();
java.io.InputStream in = FileManager.get().open(fileNameOrUri);
if (in == null) {
throw new IllegalArgumentException(fileNameOrUri + " not found");
}
if (fileNameOrUri.contains(".ttl") || fileNameOrUri.contains(".n3")) {
logger.info("Opening Turtle file");
model.read(in, null, "TTL");
} else if (fileNameOrUri.contains(".rdf")) {
logger.info("Opening RDFXML file");
model.read(in, null);
} else if (fileNameOrUri.contains(".nt")) {
logger.info("Opening N-Triples file");
model.read(in, null, "N-TRIPLE");
} else {
logger.info("Content negotiation to get RDFXML from " + fileNameOrUri);
model.read(fileNameOrUri);
}
logger.info(
"Loading "
+ fileNameOrUri
+ " is done in "
+ (System.currentTimeMillis() - startTime)
+ "ms.");
return model;
}
static String fetchPage(String[] fileNames, String ifAbsent) {
for (String fileName : fileNames) {
File f = new File(fileName);
if (f.exists()) return FileManager.get().readWholeFileAsUTF8(f.getAbsolutePath());
}
return ifAbsent;
}
public void importForMobiOfOWL(String inputFileOWL) throws Exception {
this.jena = ModelFactory.createOntologyModel();
InputStream in = FileManager.get().open(inputFileOWL);
if (in == null) throw new IllegalArgumentException("OWL file not found.");
try {
this.jena.read(in, null);
} catch (Exception ex) {
throw new ExceptionMobiFile("Problem reading the OWL file.");
}
String domainname = null;
if (this.jena.getNsPrefixMap().containsKey(this.validatorOWLGeneratedByMMobi)) {
domainname = this.jena.getNsPrefixURI(this.validatorOWLGeneratedByMMobi);
} else {
throw new ExceptionMobiFile("OWL file not generated by M-MOBI.");
}
this.mobi =
new Mobi(
domainname.substring(domainname.lastIndexOf("/") + 1, domainname.lastIndexOf("#")));
// this.ImportClassesAndInstances();
this.ImportRelationsInheritanceOrEquivalence(Relation.INHERITANCE);
this.ImportRelationsInheritanceOrEquivalence(Relation.EQUIVALENCE);
this.ImportRelationsComposition();
}
public void hospitalQueryProcess() {
Model model = ModelFactory.createDefaultModel();
InputStream in = FileManager.get().open("cancer_rdf.owl");
if (in == null) {
throw new IllegalArgumentException("File: not found");
}
// read the RDF/XML file
model.read(in, null);
for (int i = 0; i < treatment_list.size(); i++) {
String treatment_name = treatment_list.get(i);
issueSPARQLTreatment_Hospital(model, treatment_name, hos_treatment);
}
// System.out.println("Hospital list for treatments: " + Hospital_list);
System.out.println("Hospital map for treatments: " + hos_treatment);
Set set = hos_treatment.entrySet();
// Get an iterator
Iterator i = set.iterator();
// Display elements
while (i.hasNext()) {
Map.Entry me = (Map.Entry) i.next();
System.out.print(me.getKey() + ": ");
System.out.println(me.getValue());
if (!Hospital_list.contains(me.getValue().toString())) {
Hospital_list.add(me.getValue().toString());
}
}
System.out.println("Hospital list for treatments: " + Hospital_list);
model.close();
}
public Model readFile(String filename) {
// TDB.sync(dataset);
// dataset.begin(ReadWrite.WRITE);
Model model = FileManager.get().readModel(ontModel, filename, null, "RDF/XML");
// base.add(model);
// om.read(is, ns);
// dataset.commit();
// dataset.end();
return model;
}
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));
}
}
public void importOntology(String filename) {
System.out.println("Load OWL File: " + filename);
// use the FileManager to find the input file
InputStream in = FileManager.get().open(filename);
if (in == null) {
throw new IllegalArgumentException("File: " + filename + " not found");
}
// read the RDF/XML file
model.read(in, null);
}
public static void main(String args[]) {
Model model = ModelFactory.createDefaultModel();
InputStream in = FileManager.get().open(args[0]);
try {
model.read(in, null);
in.close();
System.out.println(getJSON(model));
} catch (Exception e) {
e.printStackTrace();
}
}
public void setRules(String rulesFile) {
try {
log.info("Trying to load rule file: " + rulesFile);
InputStream rulesStream = FileManager.get().open(rulesFile);
Parser rules =
Rule.rulesParserFromReader(
new BufferedReader(new InputStreamReader(rulesStream, "UTF-8")));
reasoner = new GenericRuleReasoner(Rule.parseRules(rules));
log.info("Loaded!");
} catch (Throwable ex) {
log.error("Problem loading rules <" + rulesFile + ">", ex);
}
}
@Override
@Before
public void setUp() throws Exception {
super.setUp();
folderResourceMapUri = URI.create(FOLDER_RESOURCE_MAP);
Model model =
FileManager.get()
.loadModel(folderResourceMapUri.toString(), folderResourceMapUri.toString(), "TURTLE");
dataset.addNamedModel(folderResourceMapUri.toString(), model);
folderBuilder = new FolderBuilder();
folder = researchObject.getFolders().values().iterator().next();
folderResourceMap = builder.buildFolderResourceMap(folderResourceMapUri, folder);
}
private void compareRDF(URL htmlURL, URL compareURL) throws SAXException, IOException {
String cf = compareURL.toExternalForm();
if (cf.matches("file:/[^/][^/].*")) cf = cf.replaceFirst("file:/", "file:///");
String hf = htmlURL.toExternalForm();
if (hf.matches("file:/[^/][^/].*")) hf = hf.replaceFirst("file:/", "file:///");
Model c = FileManager.get().loadModel(compareURL.toExternalForm());
Model m = ModelFactory.createDefaultModel();
StatementSink sink = new JenaStatementSink(m);
XMLReader parser = ParserFactory.createReaderForFormat(sink, Format.XHTML, Setting.OnePointOne);
parser.parse(hf);
boolean result = c.isIsomorphicWith(m);
if (!result) m.write(System.err, "TTL");
assertTrue("Files match (" + htmlURL + ")", result);
}
public void reloadOWLFile(String file) {
// create an empty model
// this.model = ModelFactory.createDefaultModel();
this.model = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
System.out.println("Load OWL File: " + file);
// use the FileManager to find the input file
InputStream in = FileManager.get().open(file);
if (in == null) {
throw new IllegalArgumentException("File: " + file + " not found");
}
// read the RDF/XML file
model.read(in, null);
}
private void executeQuery(String queryString) {
System.out.println("###########################################");
String prolog = "PREFIX vcard: <" + VCARD.getURI() + ">";
String queryStr = prolog + queryString;
Model model = ModelFactory.createDefaultModel();
InputStream in = FileManager.get().open("/home/sush/code/experiments/vc-db-3.rdf");
model.read(in, null);
Query query = QueryFactory.create(queryStr);
query.serialize(new IndentedWriter(System.out, true));
// System.out.println() ;
QueryExecution qexec = QueryExecutionFactory.create(query, model);
ResultSet rs = qexec.execSelect();
for (; rs.hasNext(); ) {
QuerySolution rb = rs.nextSolution();
System.out.println(rb);
}
}
public static Object build(String assemblerFile, Resource type) {
if (assemblerFile == null) throw new ARQException("No assembler file");
Model spec = null;
try {
spec = FileManager.get().loadModel(assemblerFile);
} catch (Exception ex) {
throw new ARQException("Failed reading assembler description: " + ex.getMessage());
}
Resource root = null;
try {
root = GraphUtils.findRootByType(spec, type);
if (root == null) return null;
} catch (TypeNotUniqueException ex) {
throw new ARQException("Multiple types for: " + DatasetAssemblerVocab.tDataset);
}
return Assembler.general.open(root);
}
public static void main(String args[]) {
String filename = "example6.rdf";
// Create an empty model
OntModel model = ModelFactory.createOntologyModel(OntModelSpec.RDFS_MEM);
// Use the FileManager to find the input file
InputStream in = FileManager.get().open(filename);
if (in == null) throw new IllegalArgumentException("File: " + filename + " not found");
// Read the RDF/XML file
model.read(in, null);
// model.write(System.out,"Turtle");
ExtendedIterator<? extends OntResource> iterator;
// ** TASK 7.1: List all individuals of "Person" **
OntClass person = model.getOntClass(ns + "Person");
iterator = person.listInstances();
System.out.println("Individuals");
System.out.println("------------------------------------");
while (iterator.hasNext()) {
OntResource r = iterator.next();
System.out.println(r.getURI());
}
System.out.println("------------------------------------");
// ** TASK 7.2: List all subclasses of "Person" **
iterator = person.listSubClasses();
System.out.println("Sublcasses");
System.out.println("------------------------------------");
while (iterator.hasNext()) {
OntResource r = iterator.next();
System.out.println(r.getURI());
}
System.out.println("------------------------------------");
// ** TASK 7.3: Make the necessary changes to get as well indirect instances and subclasses.
// TIP: you need some inference... **
}
public static void main(String args[]) {
String filename = "example6.rdf";
// Create an empty model
OntModel model = ModelFactory.createOntologyModel(OntModelSpec.RDFS_MEM);
// Use the FileManager to find the input file
InputStream in = FileManager.get().open(filename);
if (in == null) throw new IllegalArgumentException("File: " + filename + " not found");
// Read the RDF/XML file
model.read(in, null);
// ** TASK 7.1: List all individuals of "Person" **
// ** TASK 7.2: List all subclasses of "Person" **
// ** TASK 7.3: Make the necessary changes to get as well indirect instances and subclasses.
// TIP: you need some inference... **
}
static IndexLARQ buildTitleIndex(Model model, String datafile) {
// ---- Read and index just the title strings.
IndexBuilderString larqBuilder = new IndexBuilderString(DC.title);
// Index statements as they are added to the model.
model.register(larqBuilder);
// To just build the index, create a model that does not store statements
// Model model2 = ModelFactory.createModelForGraph(new GraphSink()) ;
FileManager.get().readModel(model, datafile);
// ---- Alternatively build the index after the model has been created.
// larqBuilder.indexStatements(model.listStatements()) ;
// ---- Finish indexing
larqBuilder.closeWriter();
model.unregister(larqBuilder);
// ---- Create the access index
IndexLARQ index = larqBuilder.getIndex();
return index;
}
public void createJenaModel(RegisterContextRequest rcr) {
OntModel ontModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
Model entityOnt = FileManager.get().loadModel(ONT_FILE);
ontModel.addSubModel(entityOnt);
ontModel.setNsPrefixes(entityOnt.getNsPrefixMap());
// ontModel.loadImports();
ExtendedIterator<OntProperty> iter = ontModel.listAllOntProperties();
while (iter.hasNext()) {
OntProperty ontProp = iter.next();
System.out.println(ontProp.getLocalName());
// if (formParams.containsKey(ontProp.getLocalName())) {
// regIndividual.addProperty(ontProp,
// ontModel.getcreateTypedLiteral(formParams.get(ontProp.getLocalName())[0]));
// }
}
// OntClass regClass = ontModel.getOntClass(ONT_URL + "iotReg");
// OntClass entClass = ontModel.createOntClass(ONT_URL + "entity");
// OntClass regClass = (OntClass) ontModel.createOntResource(OntClass.class,
// null,ONT_URL+"Registration" );
// OntClass regClass = (OntClass) ontModel.createClass(ONT_URL + "Registration");
// OntClass entityClass = (OntClass) ontModel.createClass(ONT_URL + "Entity");
OntClass entityGroup = (OntClass) ontModel.getOntClass(ONT_URL + "EntityGroup");
OntClass entity = (OntClass) ontModel.getOntClass(ONT_URL + "Entity");
OntClass attribute = (OntClass) ontModel.getOntClass(ONT_URL + "Attribute");
OntClass metadata = (OntClass) ontModel.getOntClass(ONT_URL + "Metadata");
OntClass location = (OntClass) ontModel.getOntClass(entityOnt.getNsPrefixURI("geo") + "Point");
// System.out.println("Class type is: " + regClass.getLocalName());
String ngsiValue = "";
ngsiValue = rcr.getRegistrationId();
Individual entityGroupIndiv = ontModel.createIndividual(ONT_URL + ngsiValue, entityGroup);
entityGroupIndiv.setPropertyValue(
ontModel.getProperty(ONT_URL + "registrationId"), ontModel.createLiteral(ngsiValue));
ngsiValue = rcr.getTimestamp().toString();
entityGroupIndiv.setPropertyValue(
ontModel.getProperty(ONT_URL + "regTimeStamp"), ontModel.createLiteral(ngsiValue));
ngsiValue = rcr.getDuration();
entityGroupIndiv.setPropertyValue(
ontModel.getProperty(ONT_URL + "duration"), ontModel.createLiteral(ngsiValue));
ngsiValue = rcr.getContextRegistration().get(0).getEntityId().get(0).getId();
Individual entity1 = ontModel.createIndividual(ONT_URL + ngsiValue, entity);
entityGroupIndiv.setPropertyValue(ontModel.getProperty(ONT_URL + "hasEntity"), entity1);
ngsiValue = rcr.getContextRegistration().get(0).getEntityId().get(0).getId();
entity1.setPropertyValue(
ontModel.getProperty(ONT_URL + "id"), ontModel.createLiteral(ngsiValue));
ngsiValue = rcr.getContextRegistration().get(0).getEntityId().get(0).getType();
entity1.setPropertyValue(
ontModel.getProperty(ONT_URL + "type"), ontModel.createLiteral(ngsiValue));
ngsiValue =
rcr.getContextRegistration().get(0).getContextRegistrationAttribute().get(0).getName();
Individual attribute1 = ontModel.createIndividual(ONT_URL + ngsiValue, attribute);
entity1.setPropertyValue(ontModel.getProperty(ONT_URL + "hasAttribute"), attribute1);
ngsiValue =
rcr.getContextRegistration().get(0).getContextRegistrationAttribute().get(0).getType();
attribute1.setPropertyValue(
ontModel.getProperty(ONT_URL + "type"), ontModel.createLiteral(ngsiValue));
ngsiValue =
rcr.getContextRegistration()
.get(0)
.getContextRegistrationAttribute()
.get(0)
.getContextMetadata()
.get(0)
.getName();
Individual metadata1 = ontModel.createIndividual(ONT_URL + ngsiValue, metadata);
attribute1.setPropertyValue(ontModel.getProperty(ONT_URL + "hasMetadata"), metadata1);
ngsiValue =
rcr.getContextRegistration()
.get(0)
.getContextRegistrationAttribute()
.get(0)
.getContextMetadata()
.get(0)
.getType();
metadata1.setPropertyValue(
ontModel.getProperty(ONT_URL + "type"), ontModel.createLiteral(ngsiValue));
ngsiValue =
rcr.getContextRegistration()
.get(0)
.getContextRegistrationAttribute()
.get(0)
.getContextMetadata()
.get(0)
.getValue()
.toString();
metadata1.setPropertyValue(
ontModel.getProperty(ONT_URL + "value"), ontModel.createLiteral(ngsiValue));
ngsiValue =
rcr.getContextRegistration()
.get(0)
.getContextRegistrationAttribute()
.get(0)
.getContextMetadata()
.get(1)
.getName();
Individual metadata2 = ontModel.createIndividual(ONT_URL + ngsiValue, metadata);
attribute1.addProperty(ontModel.getProperty(ONT_URL + "hasMetadata"), metadata2);
ngsiValue =
rcr.getContextRegistration()
.get(0)
.getContextRegistrationAttribute()
.get(0)
.getContextMetadata()
.get(1)
.getType();
metadata2.setPropertyValue(
ontModel.getProperty(ONT_URL + "type"), ontModel.createLiteral(ngsiValue));
ngsiValue =
rcr.getContextRegistration()
.get(0)
.getContextRegistrationAttribute()
.get(0)
.getContextMetadata()
.get(1)
.getValue()
.toString();
metadata2.setPropertyValue(
ontModel.getProperty(ONT_URL + "value"), ontModel.createLiteral(ngsiValue));
// ngsiValue =
// rcr.getContextRegistration().get(0).getContextRegistrationAttribute().get(0).getContextMetadata().get(2).getName();
// Individual metadata3 = ontModel.createIndividual(ONT_URL + ngsiValue, metadata);
// attribute1.addProperty(ontModel.getProperty(ONT_URL + "hasMetadata"), metadata3);
//
// ngsiValue =
// rcr.getContextRegistration().get(0).getContextRegistrationAttribute().get(0).getContextMetadata().get(2).getType();
// metadata3.setPropertyValue(ontModel.getProperty(ONT_URL + "type"),
// ontModel.createLiteral(ngsiValue));
// ngsiValue =
// rcr.getContextRegistration().get(0).getContextRegistrationAttribute().get(0).getContextMetadata().get(2).getValue().toString();
// metadata3.setPropertyValue(ontModel.getProperty(ONT_URL + "value"),
// ontModel.createLiteral(ngsiValue));
// System.out.println("has propertry
// \"expiry\":"+entityIndiv.hasProperty(ontModel.getProperty(ONT_URL, "expiry")));
ontModel.write(System.out, "TURTLE");
// ontModel.write(System.out, "RDF/XML");
// ontModel.write(System.out, "JSON-LD");
}
public static void main(String[] args) {
try {
Model schema = null;
Store store = null;
SDBConnection conn = null;
if (args.length == 1) {
store = ExtendedSDBFactory.connectStore(args[0]);
store.getTableFormatter().create();
schema = ExtendedSDBFactory.connectPagedDefaultModel(store);
} else {
StoreDesc storeDesc = new StoreDesc(args[0], args[1]);
Class.forName(args[2]);
String jdbcURL = args[3] + args[4];
conn = new SDBConnection(jdbcURL, args[5], args[6]);
store = ExtendedSDBFactory.connectStore(conn, storeDesc);
store.getTableFormatter().create();
schema = ExtendedSDBFactory.connectPagedNamedModel(store, args[7]);
}
long startTime = System.currentTimeMillis(), endTime = 0L, count = 0L;
schema.read("http://www.lehigh.edu/~zhp2/2004/0401/univ-bench.owl");
OntModel m = ExtendedModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC, schema);
String sInputDirectory = args[8];
File inputDirectory = new File(sInputDirectory);
String[] sFilenames = inputDirectory.list(new OWLFilenameFilter());
for (int i = 0; i < sFilenames.length; i++) {
InputStream in = FileManager.get().open(sInputDirectory + sFilenames[i]);
if (in == null) {
throw new IllegalArgumentException("File: " + sFilenames[i] + " not found");
}
m.read(in, "http://www.utdallas.edu/benchmark-test#", "RDF/XML-ABBREV");
in.close();
}
endTime = System.currentTimeMillis();
System.out.println("time to read the model = " + (endTime - startTime) / 1000 + " seconds.");
startTime = System.currentTimeMillis();
String queryString =
" PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> "
+ " PREFIX ub: <http://www.lehigh.edu/~zhp2/2004/0401/univ-bench.owl#> "
+ " SELECT * WHERE "
+ " { "
+ " ?x rdf:type ub:GraduateStudent . "
+ " ?x ub:takesCourse <http://www.Department0.University0.edu/GraduateCourse0> . "
+ " }";
Query query = QueryFactory.create(queryString);
QueryExecution qexec = QueryExecutionFactory.create(query, m);
ResultSet rs = qexec.execSelect();
while (rs.hasNext()) {
count++;
rs.nextSolution();
}
qexec.close();
endTime = System.currentTimeMillis();
System.out.println("count = " + count);
System.out.println("time to query = " + (endTime - startTime) + " milliseconds.");
store.close();
conn.close();
} catch (Exception e) {
e.printStackTrace();
}
}
static {
FileManager.setStdLocators(instance);
}
public Model getMappingModel() {
if (mappingModel == null && jdbcURL == null && mappingFile == null && input_mapping == null) {
throw new D2RQException("no mapping file or JDBC URL specified");
}
if (mappingModel == null && mappingFile == null) {
if (input_mapping != null) {
// gui staff
mappingModel = ModelFactory.createDefaultModel();
mappingModel.read(new StringReader(input_mapping), getResourceBaseURI(), "TURTLE");
} else {
if (d2rqMapping == null && r2rmlMapping == null) {
generateMapping();
}
StringWriter out = new StringWriter();
getWriter().write(out);
mappingModel = ModelFactory.createDefaultModel();
mappingModel.read(new StringReader(out.toString()), getResourceBaseURI(), "TURTLE");
}
}
if (mappingModel == null) {
log.info("Reading mapping file from " + mappingFile);
// Guess the language/type of mapping file based on file extension. If it is not among the
// known types then assume that the file has TURTLE syntax and force to use TURTLE parser
String lang = FileUtils.guessLang(mappingFile, "unknown");
try {
if (lang.equals("unknown")) {
mappingModel = FileManager.get().loadModel(mappingFile, getResourceBaseURI(), "TURTLE");
} else {
// if the type is known then let Jena auto-detect it and load the appropriate parser
mappingModel = FileManager.get().loadModel(mappingFile, getResourceBaseURI(), null);
}
} catch (TurtleParseException ex) {
// We have wired RIOT into Jena in the static initializer above,
// so this should never happen (it's for the old Jena Turtle/N3 parser)
throw new D2RQException("Error parsing " + mappingFile + ": " + ex.getMessage(), ex, 77);
} catch (JenaException ex) {
if (ex.getCause() != null && ex.getCause() instanceof RiotException) {
throw new D2RQException(
"Error parsing " + mappingFile + ": " + ex.getCause().getMessage(), ex, 77);
}
throw ex;
} catch (AtlasException ex) {
// Detect the specific case of non-UTF-8 encoded input files
// and do a custom error message
if (FileUtils.langTurtle.equals(lang)
&& ex.getCause() != null
&& (ex.getCause() instanceof MalformedInputException)) {
throw new D2RQException(
"Error parsing "
+ mappingFile
+ ": Turtle files must be in UTF-8 encoding; "
+ "bad encoding found at byte "
+ ((MalformedInputException) ex.getCause()).getInputLength(),
ex,
77);
}
// Generic error message for other parse errors
throw new D2RQException("Error parsing " + mappingFile + ": " + ex.getMessage(), ex, 77);
}
}
return mappingModel;
}