I wand to add an individual to a class, and I referenced the doc in OWL API official site.
Here is my code.
public void addIndividualsToClass(String className, String indName) throws OWLOntologyStorageException{
/*
* Add an individual to input class
*/
OWLClass tClass = fac.getOWLClass(IRI.create(NS + className));
OWLNamedIndividual tIndividual = fac.getOWLNamedIndividual(IRI.create(NS + indName));
OWLClassAssertionAxiom classAssertion = fac.getOWLClassAssertionAxiom(tClass, tIndividual);
manager.addAxiom(ont, classAssertion);
manager.saveOntology(ont, new StreamDocumentTarget(new ByteArrayOutputStream()));
}
Then, eclipse throws this exception.
Exception in thread "main" java.lang.IllegalArgumentException: Comparison method violates its general contract!
at java.util.ComparableTimSort.mergeLo(ComparableTimSort.java:714)
at java.util.ComparableTimSort.mergeAt(ComparableTimSort.java:451)
at java.util.ComparableTimSort.mergeCollapse(ComparableTimSort.java:376)
at java.util.ComparableTimSort.sort(ComparableTimSort.java:182)
at java.util.ComparableTimSort.sort(ComparableTimSort.java:146)
at java.util.Arrays.sort(Arrays.java:472)
at java.util.Collections.sort(Collections.java:155)
at org.coode.owlapi.owlxml.renderer.OWLXMLObjectRenderer.visit(OWLXMLObjectRenderer.java:184)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyImpl.accept(OWLOntologyImpl.java:1630)
at org.coode.owlapi.owlxml.renderer.OWLXMLRenderer.render(OWLXMLRenderer.java:106)
at org.coode.owlapi.owlxml.renderer.OWLXMLOntologyStorer.storeOntology(OWLXMLOntologyStorer.java:73)
at org.semanticweb.owlapi.util.AbstractOWLOntologyStorer.storeOntology(AbstractOWLOntologyStorer.java:174)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.saveOntology(OWLOntologyManagerImpl.java:870)
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.saveOntology(OWLOntologyManagerImpl.java:861)
at Test.addIndividualsToClass(Test.java:146)
at Test.main(Test.java:155)
Can someone help me?
This should work. You should take a look at the Examples.java on the OWL-API page at http://owlapi.sourceforge.net/index.html
public static void createNewOnto() throws OWLOntologyCreationException,
OWLOntologyStorageException {
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
IRI ontologyIRI = IRI.create("http://example.com/owlapi/families");
OWLOntology ont = manager.createOntology(ontologyIRI);
OWLDataFactory factory = manager.getOWLDataFactory();
OWLIndividual john = factory.getOWLNamedIndividual(IRI
.create(ontologyIRI + "#John"));
OWLIndividual mary = factory.getOWLNamedIndividual(IRI
.create(ontologyIRI + "#Mary"));
OWLIndividual susan = factory.getOWLNamedIndividual(IRI
.create(ontologyIRI + "#Susan"));
OWLIndividual bill = factory.getOWLNamedIndividual(IRI
.create(ontologyIRI + "#Bill"));
OWLObjectProperty hasWife = factory.getOWLObjectProperty(IRI
.create(ontologyIRI + "#hasWife"));
OWLObjectPropertyAssertionAxiom axiom1 = factory
.getOWLObjectPropertyAssertionAxiom(hasWife, john, mary);
AddAxiom addAxiom1 = new AddAxiom(ont, axiom1);
// Now we apply the change using the manager.
manager.applyChange(addAxiom1);
System.out.println("RDF/XML: ");
manager.saveOntology(ont, new StreamDocumentTarget(System.out));
}
just mentioning that some examples and methods are deprecated
The following works with version 5 of the OWL-API. It shows how to add a class assertion axiom to the ontology, i.e. asserting an individual is the instance of a class.
public void addIndividualsToClass(String className, String indName) throws Exception{
PrefixManager pm = new DefaultPrefixManager(NS); // assuming NS is string and is your namespace
OWLClass tClass = fac.getOWLClass("#" + className, pm); //assuming '#' is your delimiter
OWLIndividual tIndividual = fac.getOWLNamedIndividual("#" + indName, pm);
OWLClassAssertionAxiom classAssertion = fac.getOWLClassAssertionAxiom(tClass, tIndividual);
manager.addAxiom(ont, classAssertion);
manager.saveOntology(ont);
}
Related
I want to add an instance to my ontology file that has data attributes, but when I add dataProperty, I find that the added data cannot specify the data type.
my Code:
public final static String NAME_SPACE = "http://www.semanticweb.org/tangyuan/ontologies/myOntology#";
public static void main(String[] args) throws FileNotFoundException {
OntModel model1 = ModelFactory.createOntologyModel(OntModelSpec.OWL_DL_MEM);
model1.read("file:./myOntology.owl");
OntClass oc = model1.getOntClass(NAME_SPACE + "患者");//获得病人类
Individual individual = oc.createIndividual(NAME_SPACE + "jane");
DatatypeProperty dp = model1.getDatatypeProperty(NAME_SPACE + "twoh血糖值");
model1.add(individual, dp, "7.0");
RDFWriter rdfWriter = model1.getWriter("RDF/XML");
rdfWriter.write(model1, new FileOutputStream("myOntology.owl"), "RDF/XML");
System.out.println("ok");
}
the myontology.owl file result
<myOntology:患者 rdf:about="http://www.semanticweb.org/tangyuan/ontologies/myOntology#jane">
<myOntology:twoh血糖值>7.0</myOntology:twoh血糖值>
the dataProperty is
<myOntology:twoh血糖值>7.0</myOntology:twoh血糖值>
but I want
<myOntology:twoh血糖值 rdf:datatype="http://www.w3.org/2001/XMLSchema#float">7.0</myOntology:twoh血糖值>
how can I add
rdf:datatype="http://www.w3.org/2001/XMLSchema#float"
to the dataProperty value?
Can anyone help me. thankyou
I am trying to build a custom batch filter that extends SimpleBatchFilter. However, I am experiencing the problem of running it second time to get an inverted output. Here is the relevant code and the error I am getting after both runs are completed:
Exception in thread "main" java.lang.IndexOutOfBoundsException: Index: 79, Size: 79
at java.util.ArrayList.rangeCheck(ArrayList.java:653)
at java.util.ArrayList.get(ArrayList.java:429)
at weka.core.Attribute.addStringValue(Attribute.java:994)
at weka.core.StringLocator.copyStringValues(StringLocator.java:155)
at weka.core.StringLocator.copyStringValues(StringLocator.java:91)
at weka.filters.Filter.copyValues(Filter.java:373)
at weka.filters.Filter.push(Filter.java:290)
at weka.filters.SimpleBatchFilter.batchFinished(SimpleBatchFilter.java:266)
at weka.filters.Filter.useFilter(Filter.java:667)
at likeability.Main.main(Main.java:30)
And here is the relevant code:
public class TestFilter extends SimpleBatchFilter {
private Attribute a;
private Attribute b;
private int sampleSizePercent = 15;
private boolean invert = false;
private int seed = 1;
#Override
protected Instances process(Instances inst) throws Exception {
ArrayList<Instances> partitionsA = partition(inst, a);
ArrayList<Instances> partitions = new ArrayList<Instances>();
for(Instances data: partitionsA) {
partitions.addAll(partition(data, b));
}
return getTestSet(partitions);
}
/*
* Partitions the data so that there's only one nominal value of the
* attribute a in one partition.
*/
private ArrayList<Instances> partition(Instances data, Attribute att) throws Exception {
ArrayList<Instances> instances = new ArrayList<Instances>();
for (int i = 0; i < att.numValues(); i++){
RemoveWithValues rm = new RemoveWithValues();
rm.setAttributeIndex(Integer.toString(att.index()+1));
rm.setInvertSelection(true);
rm.setNominalIndices(Integer.toString(i+1));
rm.setInputFormat(data);
instances.add(Filter.useFilter(data, rm));
}
return instances;
}
private Instances getTestSet(List<Instances> insts) throws Exception {
Instances output = new Instances(insts.get(0), 0);
for(Instances inst: insts) {
Resample filter = new Resample();
filter.setRandomSeed(seed);
filter.setNoReplacement(true);
filter.setInvertSelection(invert);
filter.setSampleSizePercent(sampleSizePercent);
filter.setInputFormat(inst);
Instances curr = Filter.useFilter(inst, filter);
System.out.println(inst.size() + " " + curr.size());
output.addAll(curr);
}
return output;
}
#Override
protected Instances determineOutputFormat(Instances arg) throws Exception {
return new Instances(arg, 0);
}
#Override
public String globalInfo() {
return "A filter which partitions the data so that each partition contains"
+ " only instances with one value of attribute a and b, then takes "
+ "a random subset of values from each partition and merges them to"
+ " produce the final set.";
}
public Capabilities getCapabilities() {
Capabilities result = super.getCapabilities();
result.enableAllAttributes();
result.enableAllClasses();
result.enable(Capability.NO_CLASS); // filter doesn't need class to be set
return result;
}
//Main and getters and setters
}
And this is how I call it:
TestFilter filter = new TestFilter();
filter.setA(data.attribute("gender"));
filter.setB(data.attribute("age"));
filter.setInputFormat(data);
Instances test = Filter.useFilter(data, filter);
filter.setInvert(true);
filter.setInputFormat(data);
Instances train = Filter.useFilter(data, filter);
It seems to me quite stupid that I would need to use those two lines between the calls. I suspect I should use isBatchFinished(), does it mean I have to implement it extending BatchFilter rather then SimpleBatchFilter? It would be also helpful to see some successful implementations, since the only ones I could find where the ones in the WEKA manual.
I solved it by extending a Filter instead and changing the process function to batchFinished(). I am posting this answer as I have not found a custom filter example anywhere else.
#Override
public boolean batchFinished() throws Exception {
if(isFirstBatchDone()) {
invert = true;
}
if (getInputFormat() == null)
throw new NullPointerException("No input instance format defined");
Instances inst = getInputFormat();
ArrayList<Instances> partitionsA = partition(inst, a);
ArrayList<Instances> partitions = new ArrayList<Instances>();
for(Instances data: partitionsA) {
partitions.addAll(partition(data, b));
}
private void getTestSet(List<Instances> insts) throws Exception {
for(Instances inst: insts) {
Resample filter = new Resample();
filter.setRandomSeed(seed);
filter.setNoReplacement(true);
filter.setInvertSelection(invert);
filter.setSampleSizePercent(sampleSizePercent);
filter.setInputFormat(inst);
Instances curr = Filter.useFilter(inst, filter);
System.out.println(inst.size() + " " + curr.size());
curr.forEach((i) -> push(i));
}
}
#Override
public boolean setInputFormat(Instances arg) throws Exception {
super.setInputFormat(arg);
Instances outputFormat = new Instances(arg, 0);
setOutputFormat(outputFormat);
return true;
}
I'm new to java and I have a problem with reading a file using the scanner class.
My objective is to read the following .txt file:
3
Emmalaan 23
3051JC Rotterdam
7 rooms
price 300000
Javastraat 88
4078KB Eindhoven
3 rooms
price 50000
Javastraat 93
4078KB Eindhoven
4 rooms
price 55000
The "3" on top of the file should be read as an integer that tells how many houses the file has. The following four lines after the "3" determine one house.
I try to read this file using a read method in the class portefeuille:
public static Portefeuille read(String infile)
{
Portefeuille returnvalue = new Portefeuille();
try
{
Scanner scan = new Scanner(new File(infile)).useDelimiter(" |/n");
int aantalwoningen = scan.nextInt();
for(int i = 0; i<aantalwoningen; ++i)
{
Woning.read(scan);
}
}
catch (FileNotFoundException e)
{
System.out.println("File could not be found");
}
catch (IOException e)
{
System.out.println("Exception while reading the file");
}
return returnvalue;
}
The read method in the Woning class looks like this:
public static Woning read(Scanner sc)
{
String token_adres = sc.next();
String token_dr = sc.next();
String token_postcd = sc.next();
String token_plaats = sc.next();
int token_vraagPrijs = sc.nextInt();
String token_kamerstxt = sc.next();
String token_prijstxt = sc.next();
int token_kamers = sc.nextInt();
return new Woning(adresp, token_vraagPrijs, token_kamers);
}
When I try to execute the following code:
Portefeuille port1 = Portefeuille.read("woningen.txt");
I get the following error:
Exception in thread "main" java.util.InputMismatchException
at java.util.Scanner.throwFor(Scanner.java:840)
at java.util.Scanner.next(Scanner.java:1461)
at java.util.Scanner.nextInt(Scanner.java:2091)
at java.util.Scanner.nextInt(Scanner.java:2050)
at Portefeuille.read(Portefeuille.java:48)
at Portefeuille.main(Portefeuille.java:112)
However if I use the read method from the Woning class to read one adres in a string format:
Emmalaan 23
3051JC Rotterdam
7 Rooms
price 300000
It works fine.
I tried to change the .txt file into only one address without the "3" on top so that it is exactly formatted like the address that should work. But when I call the read method from Woning class it still gives me the error.
Could anyone please help me with this?
Thank you!
I was also facing a similar issue, so I put my answer so that it could help in future:
There are two possible modifications which I did to make this code run.
First option: Change the use of useDelimiter method to .useDelimiter("\\r\\n") when creating the Scanner class, I was in windows so we might need \\r for Windows compatibility.
Using this modification, there will be no exception.But the code will again fail at int token_vraagPrijs = sc.nextInt();.
Because in the public static Woning read(Scanner sc), you are suing sc.next();.Actually this method finds and returns the next complete token from this scanner.A complete token is preceded and followed by input that matches the delimiter pattern.
So, every sc.next() is actually reading a line not a token.
So as per your code sc.nextInt() is trying to read something like Javastraat 88.So again it will give you the same exception.
Second option (Preferred):Don't use any delimiter, Scanner class will default whitespace and your code will work fine.I modified your code and It worked fine for me.
Code:
public class Test3{
public static void main(String... s)
{
read("test.txt");
}
public static void read(String infile)
{
try (Scanner scan = new Scanner(new File(infile)))
{
int aantalwoningen = scan.nextInt();
System.out.println(aantalwoningen);
for (int i = 0; i < aantalwoningen; ++i)
{
read(scan);
}
}
catch (FileNotFoundException e)
{
System.out.println("File could not be found");
}
}
public static void read(Scanner sc)
{
String token_adres = sc.next();
String token_dr = sc.next();
String token_postcd = sc.next();
String token_plaats = sc.next();
int token_vraagPrijs = sc.nextInt();
String token_kamerstxt = sc.next();
String token_prijstxt = sc.next();
int token_kamers = sc.nextInt();
System.out.println(token_adres + " " + token_dr + " " + token_postcd + " " + token_plaats + " "
+ token_vraagPrijs + " " + token_kamerstxt + " " + token_prijstxt + " " + token_kamers);
} }
I have an SIU S12 message that does not contain a PV2 segment. However, when I get the parsed message from NHAPI, the parent group for PV2, the SIU_S12_PATIENT group, return 1 for currentReps ("PV2"), which means the PV2 is present.
var parser = new NHapi.Base.Parser.PipeParser();
var parsedMessage = parser.Parse(message) as NHapi.Model.V231.Message.SIU_S12;
var patientGroup=parsedMessage.GetPATIENT(0);
// This call should not create the segment if it does not exist
int pv2Count=patientGroup.currentReps("PV2");
//pv2Count is 1 here despite no PV2 segment exists in the message
//also Both GetAll("PV2") and SegmentFinder say the PV2 segment is present
//DG1RepetitionsUsed is also 1 despite no DG1 segment is present in the message
I am trying to avoid writing code to evaluate every field in the segment. PV2 is just an example - there are a lot more segments that could be missing from the message source.
I am using NHAPI v 2.4, the latest version.
Update: following Tyson's suggestion I come up with this method；
var parser = new NHapi.Base.Parser.PipeParser();
var parsedMessage = parser.Parse(message) as NHapi.Model.V231.Message.SIU_S12;
var encodingChars = new NHapi.Base.Parser.EncodingCharacters('|', null);
var patientGroup = parsedMessage.GetPATIENT(0);
var dg1 = (NHapi.Model.V231.Segment.DG1) (patientGroup.GetStructure("DG1"));
string encodedDg1 = NHapi.Base.Parser.PipeParser.Encode(dg1, encodingChars);
bool dg1Exists = string.Compare(encodedDg1,
"DG1", StringComparison.InvariantCultureIgnoreCase)==0;
easiest thing that I have found to do is to determine if a segment is in a message is to search the actual string of the message for the segment name plus a pipe. So, for example
if(message.Contains("PV2|"))
{
//do something neat
}
From my experience, it is either that, or examining every sub-field under the segment to see if there is a value.
EDIT
I found another way to check that might work a little better. The PipeParser class has a couple of static methods on it that takes in ISegment, IGroup, and IType objects that will return a string representation of the object NHapi reference.
Sample code:
string validTestMessages =
"MSH|^~\\&|ADT1|MCM|LABADT|MCM|198808181126|SECURITY|ADT^A01|MSG00001|P|2.6\r" +
"EVN|A01-|198808181123\r" +
"PID|||PID1234^5^M11^HBOC^CPI^HV||JONES^WILLIAM^A^III||19610615000000|M||2106-3|1200 N ELM STREET^^GREENSBORO^NC^27401-1020|GL||||S||S|123456789|9-87654^NC\r" +
"PV1|1|I|||||TEST^TEST^TEST||||||||||||||||||||||||||||||||||||||||||||\r";
var encodingChars = new EncodingCharacters('|', null);
PipeParser parser = new PipeParser();
var message = parser.Parse(validTestMessages);
PV1 pv1 = (PV1)message.GetStructure("PV1");
var doctor = pv1.GetAttendingDoctor(0);
string encodedMessage = PipeParser.Encode(pv1, encodingChars);
Console.WriteLine(encodedMessage);
encodedMessage = PipeParser.Encode(doctor, encodingChars);
Console.WriteLine(encodedMessage);
Output:
PV1|1|I|||||TEST^TEST^TEST
TEST^TEST^TEST
if there is no segment or the item is empty, then the PiperParser will return an empty string.
You can read segment line by line to a file and add in hl7 Record object and check segment exist or not.
package com.sachan.ranvijay#gmail.com.hl7.msg;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import org.nule.lighthl7lib.hl7.Hl7Record;
import org.nule.lighthl7lib.hl7.Hl7Segment;
import com.stpl.hl7.dto.HL7PatientInfoDTO;
/**
* This class will parse the hl7 message. it can accept message file in the format of java.io.file
* as well as String. Its Uses org.nule.lighthl7lib.hl7.Hl7Record
* as a main component.
* #author Ranvijay.Singh
*
*/
public class PrepareHL7Message {
StringBuilder hl7Msg = new StringBuilder();
Hl7Record record = null;
public PrepareHL7Message(File file) throws Exception {
BufferedReader reader = new BufferedReader(
new FileReader(file));
String str = reader.readLine();
while (str != null) {
hl7Msg.append(str).append("\r");
str = reader.readLine();
}
reader.close();
try{
record = new Hl7Record(hl7Msg.toString());
}catch (Exception e) {
throw e;
}
}
public PrepareHL7Message(String msg) throws Exception {
try{
record = new Hl7Record(msg);
}catch (Exception e) {
throw e;
}
}
private HL7PatientInfoDTO getPatientOrderingPhysician(HL7PatientInfoDTO padto) {
Hl7Segment seg = record.getSegment("PV1");
if(seg!=null)
padto.setOrderingPhysician(seg.field(7).toString());
return padto;
}
}
//DTO.............
package com.sachan.ranvijay#gmail.com.hl7.dto;
public class HL7PatientInfoDTO {
/**
* maped with PV1-7
*/
private String orderingPhysician;
/**
* #return the orderingPhysician
*/
public String getOrderingPhysician() {
return orderingPhysician;
}
/**
* #param orderingPhysician the orderingPhysician to set
*/
public void setOrderingPhysician(String orderingPhysician) {
this.orderingPhysician = orderingPhysician;
}
}
EntityManager em = getEntityManager();
EntityTransaction etx = em.getTransaction();
etx.begin();
Query query = em.createNamedQuery("login_procedure").setParameter("param1","user").setParameter("param2", "pw");
Integer result = 23;
try {
System.out.println("query = " + query.getSingleResult());
} catch (Exception e) {
result = null;
e.printStackTrace();
}
etx.commit();
em.close();
...executing this code I get
[EL Warning]: 2011-02-10 17:32:16.846--UnitOfWork(1267140342)--Exception
[EclipseLink-4002] (Eclipse
Persistence Services -
1.2.0.v20091016-r5565): org.eclipse.persistence.exceptions.DatabaseException
Internal Exception:
org.firebirdsql.jdbc.FBSQLException:
GDS Exception. 335544569. Dynamic SQL
Error SQL error code = -104 Token
unknown - line 1, column 36
= Error Code: 335544569 Call: EXECUTE PROCEDURE LOGIN_PROCEDURE(USER_NAME =
?, USER_PASSWORD = ?) bind => [user,
pw] Query:
DataReadQuery(name="login_procedure" )
The -104 SQL error usually indicates a SQL syntax error.
Everything is processed without any error until query.getSingleResult() is called. Calling query.getResultList() doesn't change anything. I've tried several 1.x and 2.x EclipseLink versions. The Firebird DB version is 2.1.
The JPA2 declaration is:
#Entity
#NamedStoredProcedureQuery(
name = "login_procedure",
resultClass = void.class,
procedureName = "LOGIN_PROCEDURE",
returnsResultSet = false,
parameters = {
#StoredProcedureParameter(queryParameter = "param1", name = "USER_NAME", direction = Direction.IN, type = String.class),
#StoredProcedureParameter(queryParameter = "param2", name = "USER_PASSWORD", direction = Direction.IN, type = String.class)
}
)
#Table(name = "USERS")
public class Login implements Serializable {
#Id
private Long id;
}
UPDATE:
After tinkering a little bit more, I believe there might be an error in the EclipseLink implementation as EXECUTE PROCEDURE LOGIN_PROCEDURE(USER_NAME = ?, USER_PASSWORD = ?) isn't valid Firebird 2.1 syntax for calling procedures.
By specifying the name="USER_NAME" you are making Eclipselink use the 'USER_NAME=?' syntax instead of just passing in the unnamed parameter. Try removing the name definition.
Inspired by this post, I've found a solution/workaround:
public class JPATest {
final Session session;
JPATest() {
final String DATABASE_USERNAME = "SYSDBA";
final String DATABASE_PASSWORD = "masterkey";
final String DATABASE_URL = "jdbc:firebirdsql:dbServer/3050:e:/my/db.fdb";
final String DATABASE_DRIVER = "org.firebirdsql.jdbc.FBDriver";
final DatabaseLogin login = new DatabaseLogin();
login.setUserName(DATABASE_USERNAME);
login.setPassword(DATABASE_PASSWORD);
login.setConnectionString(DATABASE_URL);
login.setDriverClassName(DATABASE_DRIVER);
login.setDatasourcePlatform(new FirebirdPlatform());
login.bindAllParameters();
final Project project = new Project(login);
session = project.createDatabaseSession();
session.setLogLevel(SessionLog.FINE);
((DatabaseSession) session).login();
}
public static void main(String[] args) {
final JPATest jpaTest = new JPATest();
jpaTest.run();
}
protected void run() {
testProcCursor();
}
/*
* Run Proc with scalar input and cursor output
*/
#SuppressWarnings("unchecked")
private void testProcCursor() {
final StoredProcedureCall call = new StoredProcedureCall();
call.setProcedureName("LOGIN");
call.addUnamedArgument("USER_NAME"); // .addNamedArgument doesn't work
call.addUnamedArgument("USER_PASSWORD");
final DataReadQuery query = new DataReadQuery();
query.setCall(call);
query.addArgument("USER_NAME");
query.addArgument("USER_PASSWORD");
final List<String> queryArgs = new ArrayList<String>();
queryArgs.add("onlinetester");
queryArgs.add("test");
final List outList = (List) session.executeQuery(query, queryArgs);
final ListIterator<DatabaseRecord> listIterator = ((List<DatabaseRecord>) outList).listIterator();
while (listIterator.hasNext()) {
final DatabaseRecord databaseRecord = listIterator.next();
System.out.println("Value -->" + databaseRecord.getValues());
}
}
}
Apparently named parameters aren't supported in my specific configuration but using unnamed parameters in annotations, hasn't solved the problem either. However using unnamed parameters, as specified above, solved the problem for me.