OWL-S Precondition expression extracting - expression

I am trying to extract the precondition's expression as SWRL to make a IOPE web service OWL-S matchmaking
Here's my code
final OWLIndividualList<Condition> cs = service.getProcess().getConditions();
final ArrayList<ArrayList<URI>> conditions = new ArrayList<ArrayList<URI>>();
for (final Condition<?> c : cs){
if (c.canCastTo(Condition.SWRL.class)){
final Condition.SWRL sc = c.castTo(Condition.SWRL.class);
for (final Atom a : sc.getBody()){
a.accept(new AtomVisitor() {
public void visit(final IndividualPropertyAtom atom){
URI aux = null;
final ArrayList<URI> uris = new ArrayList<URI>();
URI a1 = aux.create((atom.getArgument1().getNamespace().toString()
+atom.getArgument1().toString()));
URI a2 = aux.create((atom.getArgument2().getNamespace().toString()
+atom.getArgument2().toString()));
URI p = aux.create(atom.getPropertyPredicate().toString());
uris.add(p);
uris.add(a1);
uris.add(a2);
conditions.add(uris);
}
public void visit(final DataPropertyAtom atom) { }
public void visit(final SameIndividualAtom atom) { }
public void visit(final DifferentIndividualsAtom atom) { }
public void visit(final ClassAtom atom) { }
public void visit(final BuiltinAtom atom) { }
});
}
}
}
I am getting an java.lang.NullPointerException on "final Atom a : sc.getBody()"
The OWL-S precondition statement
<expr:SWRL-Condition rdf:ID="DifferentLocations">
<expr:expressionLanguage rdf:resource="http://www.daml.org/services/owl-
s/1.2/generic/Expression.owl#SWRL"/>
<expr:expressionBody rdf:parseType="Literal">
<swrl:AtomList>
<rdf:first>
<swrl:DifferentIndividualsAtom>
<swrl:argument1 rdf:resource="#_GEOPOLITICAL-ENTITY"/>
<swrl:argument2 rdf:resource="#_GEOPOLITICAL-ENTITY1"/>
</swrl:DifferentIndividualsAtom>
</rdf:first>
<rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
</swrl:AtomList>
</expr:expressionBody>
</expr:SWRL-Condition>
Please I need help

This issue is not linked to the java code but to the OWLS-S file syntaxe. you can resolve this issue by replacing:
<expr:expressionBody rdf:parseType="Literal">
which hold the SWRL precondition (or eventually the result), by:
<expr:expressionObject>

Related

RestControllerAdvice access to request path

wanting to use RestControllerAdvice and in like the default response from Spring have the path. Seems like via the ExceptionHandler I can use the WebRequest.
I can see the headers but unsure how to show the path. looked at the parameters but nothing in there showed the path. How can I obtain the path of the request:
#RestControllerAdvice
public class RestControllerExceptionHandler {
#Autowired
private ErrorAttributesConfig errAttrib;
#ExceptionHandler(value = {IOException.class})
#ResponseStatus(HttpStatus.BANDWIDTH_LIMIT_EXCEEDED)
public AppErrorAttributes internalServerError(Exception e, WebRequest h) {
System.out.println(h.getContextPath());
// for (Iterator<String> i = h.getParameterNames(); i.hasNext(); ) {
// System.out.println(i.next());
// }
String[] s = h.getAttributeNames(0);
for (Iterator<String> i = h.getHeaderNames(); i.hasNext();) {
System.out.println(i.next());
}
AppErrorAttributes aea = errAttrib.appErrorAttributes();
aea.setStatus(HttpStatus.BAD_REQUEST.value());
aea.setError(HttpStatus.BAD_REQUEST.getReasonPhrase());
aea.setMessage(e.getMessage());
return aea;
}
used
#ExceptionHandler(value = {IOException.class})
#ResponseStatus(HttpStatus.BANDWIDTH_LIMIT_EXCEEDED)
// public AppErrorAttributes internalServerError(Exception e, WebRequest h) {
public AppErrorAttributes internalServerError(Exception e, HttpServletRequest h) {
System.out.println(h.getServletPath());
System.out.println(h.getRequestURI());

Java 8 - Streams - exception handling is mandatory in stream processing? [duplicate]

I know how to create a reference to a method that has a String parameter and returns an int, it's:
Function<String, Integer>
However, this doesn't work if the function throws an exception, say it's defined as:
Integer myMethod(String s) throws IOException
How would I define this reference?
You'll need to do one of the following.
If it's your code, then define your own functional interface that declares the checked exception:
#FunctionalInterface
public interface CheckedFunction<T, R> {
R apply(T t) throws IOException;
}
and use it:
void foo (CheckedFunction f) { ... }
Otherwise, wrap Integer myMethod(String s) in a method that doesn't declare a checked exception:
public Integer myWrappedMethod(String s) {
try {
return myMethod(s);
}
catch(IOException e) {
throw new UncheckedIOException(e);
}
}
and then:
Function<String, Integer> f = (String t) -> myWrappedMethod(t);
or:
Function<String, Integer> f =
(String t) -> {
try {
return myMethod(t);
}
catch(IOException e) {
throw new UncheckedIOException(e);
}
};
You can actually extend Consumer (and Function etc.) with a new interface that handles exceptions -- using Java 8's default methods!
Consider this interface (extends Consumer):
#FunctionalInterface
public interface ThrowingConsumer<T> extends Consumer<T> {
#Override
default void accept(final T elem) {
try {
acceptThrows(elem);
} catch (final Exception e) {
// Implement your own exception handling logic here..
// For example:
System.out.println("handling an exception...");
// Or ...
throw new RuntimeException(e);
}
}
void acceptThrows(T elem) throws Exception;
}
Then, for example, if you have a list:
final List<String> list = Arrays.asList("A", "B", "C");
If you want to consume it (eg. with forEach) with some code that throws exceptions, you would traditionally have set up a try/catch block:
final Consumer<String> consumer = aps -> {
try {
// maybe some other code here...
throw new Exception("asdas");
} catch (final Exception ex) {
System.out.println("handling an exception...");
}
};
list.forEach(consumer);
But with this new interface, you can instantiate it with a lambda expression and the compiler will not complain:
final ThrowingConsumer<String> throwingConsumer = aps -> {
// maybe some other code here...
throw new Exception("asdas");
};
list.forEach(throwingConsumer);
Or even just cast it to be more succinct!:
list.forEach((ThrowingConsumer<String>) aps -> {
// maybe some other code here...
throw new Exception("asda");
});
Update
Looks like there's a very nice utility library part of Durian called Errors which can be used to solve this problem with a lot more flexibility. For example, in my implementation above I've explicitly defined the error handling policy (System.out... or throw RuntimeException), whereas Durian's Errors allow you to apply a policy on the fly via a large suite of utility methods. Thanks for sharing it, #NedTwigg!.
Sample usage:
list.forEach(Errors.rethrow().wrap(c -> somethingThatThrows(c)));
I think Durian's Errors class combines many of the pros of the various suggestions above.
Wrap a throwing function to a standard Java 8 functional interface.
Easily specify various policies for handling errors
When wrapping a method that returns a value, there is an important distinction between specifying a default value or rethrowing a RuntimeException.
Throwing versions of Java 8's functional interfaces
Similar to fge's answer
Standard interfaces for throwing specific exceptions
Which addresses Zoltán's concern
To include Durian in your project, you can either:
grab it from jcenter or maven central at com.diffplug.durian:durian:3.3.0
or just copy paste just two small classes into your code: Throwing.java and Errors.java
This is not specific to Java 8. You are trying to compile something equivalent to:
interface I {
void m();
}
class C implements I {
public void m() throws Exception {} //can't compile
}
Disclaimer: I haven't used Java 8 yet, only read about it.
Function<String, Integer> doesn't throw IOException, so you can't put any code in it that throws IOException. If you're calling a method that expects a Function<String, Integer>, then the lambda that you pass to that method can't throw IOException, period. You can either write a lambda like this (I think this is the lambda syntax, not sure):
(String s) -> {
try {
return myMethod(s);
} catch (IOException ex) {
throw new RuntimeException(ex);
// (Or do something else with it...)
}
}
Or, if the method you're passing the lambda to is one you wrote yourself, you can define a new functional interface and use that as the parameter type instead of Function<String, Integer>:
public interface FunctionThatThrowsIOException<I, O> {
O apply(I input) throws IOException;
}
If you don't mind to use a 3rd party lib (Vavr) you could write
CheckedFunction1<String, Integer> f = this::myMethod;
It also has the so-called Try monad which handles errors:
Try(() -> f.apply("test")) // results in a Success(Integer) or Failure(Throwable)
.map(i -> ...) // only executed on Success
...
Please read more here.
Disclaimer: I'm the creator of Vavr.
Sneaky throw idiom enables bypassing CheckedException of Lambda expression. Wrapping a CheckedException in a RuntimeException is not good for strict error handling.
It can be used as a Consumer function used in a Java collection.
Here is a simple and improved version of jib's answer.
import static Throwing.rethrow;
#Test
public void testRethrow() {
thrown.expect(IOException.class);
thrown.expectMessage("i=3");
Arrays.asList(1, 2, 3).forEach(rethrow(e -> {
int i = e.intValue();
if (i == 3) {
throw new IOException("i=" + i);
}
}));
}
This just wrapps the lambda in a rethrow. It makes CheckedException rethrow any Exception that was thrown in your lambda.
public final class Throwing {
private Throwing() {}
#Nonnull
public static <T> Consumer<T> rethrow(#Nonnull final ThrowingConsumer<T> consumer) {
return consumer;
}
/**
* The compiler sees the signature with the throws T inferred to a RuntimeException type, so it
* allows the unchecked exception to propagate.
*
* http://www.baeldung.com/java-sneaky-throws
*/
#SuppressWarnings("unchecked")
#Nonnull
public static <E extends Throwable> void sneakyThrow(#Nonnull Throwable ex) throws E {
throw (E) ex;
}
}
Find a complete code and unit tests here.
You could however create your own FunctionalInterface that throws as below..
#FunctionalInterface
public interface UseInstance<T, X extends Throwable> {
void accept(T instance) throws X;
}
then implement it using Lambdas or references as shown below.
import java.io.FileWriter;
import java.io.IOException;
//lambda expressions and the execute around method (EAM) pattern to
//manage resources
public class FileWriterEAM {
private final FileWriter writer;
private FileWriterEAM(final String fileName) throws IOException {
writer = new FileWriter(fileName);
}
private void close() throws IOException {
System.out.println("close called automatically...");
writer.close();
}
public void writeStuff(final String message) throws IOException {
writer.write(message);
}
//...
public static void use(final String fileName, final UseInstance<FileWriterEAM, IOException> block) throws IOException {
final FileWriterEAM writerEAM = new FileWriterEAM(fileName);
try {
block.accept(writerEAM);
} finally {
writerEAM.close();
}
}
public static void main(final String[] args) throws IOException {
FileWriterEAM.use("eam.txt", writerEAM -> writerEAM.writeStuff("sweet"));
FileWriterEAM.use("eam2.txt", writerEAM -> {
writerEAM.writeStuff("how");
writerEAM.writeStuff("sweet");
});
FileWriterEAM.use("eam3.txt", FileWriterEAM::writeIt);
}
void writeIt() throws IOException{
this.writeStuff("How ");
this.writeStuff("sweet ");
this.writeStuff("it is");
}
}
You can use unthrow wrapper
Function<String, Integer> func1 = s -> Unthrow.wrap(() -> myMethod(s));
or
Function<String, Integer> func2 = s1 -> Unthrow.wrap((s2) -> myMethod(s2), s1);
You can.
Extending #marcg 's UtilException and adding generic <E extends Exception> where necessary: this way, the compiler will force you again to add throw clauses and everything's as if you could throw checked exceptions natively on java 8's streams.
public final class LambdaExceptionUtil {
#FunctionalInterface
public interface Function_WithExceptions<T, R, E extends Exception> {
R apply(T t) throws E;
}
/**
* .map(rethrowFunction(name -> Class.forName(name))) or .map(rethrowFunction(Class::forName))
*/
public static <T, R, E extends Exception> Function<T, R> rethrowFunction(Function_WithExceptions<T, R, E> function) throws E {
return t -> {
try {
return function.apply(t);
} catch (Exception exception) {
throwActualException(exception);
return null;
}
};
}
#SuppressWarnings("unchecked")
private static <E extends Exception> void throwActualException(Exception exception) throws E {
throw (E) exception;
}
}
public class LambdaExceptionUtilTest {
#Test
public void testFunction() throws MyTestException {
List<Integer> sizes = Stream.of("ciao", "hello").<Integer>map(rethrowFunction(s -> transform(s))).collect(toList());
assertEquals(2, sizes.size());
assertEquals(4, sizes.get(0).intValue());
assertEquals(5, sizes.get(1).intValue());
}
private Integer transform(String value) throws MyTestException {
if(value==null) {
throw new MyTestException();
}
return value.length();
}
private static class MyTestException extends Exception { }
}
I had this problem with Class.forName and Class.newInstance inside a lambda, so I just did:
public Object uncheckedNewInstanceForName (String name) {
try {
return Class.forName(name).newInstance();
}
catch (ClassNotFoundException | InstantiationException | IllegalAccessException e) {
throw new RuntimeException(e);
}
}
Inside the lambda, instead of calling Class.forName("myClass").newInstance() I just called uncheckedNewInstanceForName ("myClass")
Create a custom return type that will propagate the checked exception. This is an alternative to creating a new interface that mirrors the existing functional interface with the slight modification of a "throws exception" on the functional interface's method.
Definition
CheckedValueSupplier
public static interface CheckedValueSupplier<V> {
public V get () throws Exception;
}
CheckedValue
public class CheckedValue<V> {
private final V v;
private final Optional<Exception> opt;
public Value (V v) {
this.v = v;
}
public Value (Exception e) {
this.opt = Optional.of(e);
}
public V get () throws Exception {
if (opt.isPresent()) {
throw opt.get();
}
return v;
}
public Optional<Exception> getException () {
return opt;
}
public static <T> CheckedValue<T> returns (T t) {
return new CheckedValue<T>(t);
}
public static <T> CheckedValue<T> rethrows (Exception e) {
return new CheckedValue<T>(e);
}
public static <V> CheckedValue<V> from (CheckedValueSupplier<V> sup) {
try {
return CheckedValue.returns(sup.get());
} catch (Exception e) {
return Result.rethrows(e);
}
}
public static <V> CheckedValue<V> escalates (CheckedValueSupplier<V> sup) {
try {
return CheckedValue.returns(sup.get());
} catch (Exception e) {
throw new RuntimeException(e);
}
}
}
Usage
// Don't use this pattern with FileReader, it's meant to be an
// example. FileReader is a Closeable resource and as such should
// be managed in a try-with-resources block or in another safe
// manner that will make sure it is closed properly.
// This will not compile as the FileReader constructor throws
// an IOException.
Function<String, FileReader> sToFr =
(fn) -> new FileReader(Paths.get(fn).toFile());
// Alternative, this will compile.
Function<String, CheckedValue<FileReader>> sToFr = (fn) -> {
return CheckedValue.from (
() -> new FileReader(Paths.get("/home/" + f).toFile()));
};
// Single record usage
// The call to get() will propagate the checked exception if it exists.
FileReader readMe = pToFr.apply("/home/README").get();
// List of records usage
List<String> paths = ...; //a list of paths to files
Collection<CheckedValue<FileReader>> frs =
paths.stream().map(pToFr).collect(Collectors.toList());
// Find out if creation of a file reader failed.
boolean anyErrors = frs.stream()
.filter(f -> f.getException().isPresent())
.findAny().isPresent();
What's going on?
A single functional interface that throws a checked exception is created (CheckedValueSupplier). This will be the only functional interface which allows checked exceptions. All other functional interfaces will leverage the CheckedValueSupplier to wrap any code that throws a checked exception.
The CheckedValue class will hold the result of executing any logic that throws a checked exception. This prevents propagation of a checked exception until the point at which code attempts to access the value that an instance of CheckedValue contains.
The problems with this approach.
We are now throwing "Exception" effectively hiding the specific type originally thrown.
We are unaware that an exception occurred until CheckedValue#get() is called.
Consumer et al
Some functional interfaces (Consumer for example) must be handled in a different manner as they don't provide a return value.
Function in lieu of Consumer
One approach is to use a function instead of a consumer, which applies when handling streams.
List<String> lst = Lists.newArrayList();
// won't compile
lst.stream().forEach(e -> throwyMethod(e));
// compiles
lst.stream()
.map(e -> CheckedValueSupplier.from(
() -> {throwyMethod(e); return e;}))
.filter(v -> v.getException().isPresent()); //this example may not actually run due to lazy stream behavior
Escalate
Alternatively, you can always escalate to a RuntimeException. There are other answers that cover escalation of a checked exception from within a Consumer.
Don't consume.
Just avoid functional interfaces all together and use a good-ole-fashioned for loop.
Another solution using a Function wrapper would be to return either an instance of a wrapper of your result, say Success, if everything went well, either an instance of, say Failure.
Some code to clarify things :
public interface ThrowableFunction<A, B> {
B apply(A a) throws Exception;
}
public abstract class Try<A> {
public static boolean isSuccess(Try tryy) {
return tryy instanceof Success;
}
public static <A, B> Function<A, Try<B>> tryOf(ThrowableFunction<A, B> function) {
return a -> {
try {
B result = function.apply(a);
return new Success<B>(result);
} catch (Exception e) {
return new Failure<>(e);
}
};
}
public abstract boolean isSuccess();
public boolean isError() {
return !isSuccess();
}
public abstract A getResult();
public abstract Exception getError();
}
public class Success<A> extends Try<A> {
private final A result;
public Success(A result) {
this.result = result;
}
#Override
public boolean isSuccess() {
return true;
}
#Override
public A getResult() {
return result;
}
#Override
public Exception getError() {
return new UnsupportedOperationException();
}
#Override
public boolean equals(Object that) {
if(!(that instanceof Success)) {
return false;
}
return Objects.equal(result, ((Success) that).getResult());
}
}
public class Failure<A> extends Try<A> {
private final Exception exception;
public Failure(Exception exception) {
this.exception = exception;
}
#Override
public boolean isSuccess() {
return false;
}
#Override
public A getResult() {
throw new UnsupportedOperationException();
}
#Override
public Exception getError() {
return exception;
}
}
A simple use case :
List<Try<Integer>> result = Lists.newArrayList(1, 2, 3).stream().
map(Try.<Integer, Integer>tryOf(i -> someMethodThrowingAnException(i))).
collect(Collectors.toList());
This problem has been bothering me as well; this is why I have created this project.
With it you can do:
final ThrowingFunction<String, Integer> f = yourMethodReferenceHere;
There are a totla of 39 interfaces defined by the JDK which have such a Throwing equivalent; those are all #FunctionalInterfaces used in streams (the base Stream but also IntStream, LongStream and DoubleStream).
And as each of them extend their non throwing counterpart, you can directly use them in lambdas as well:
myStringStream.map(f) // <-- works
The default behavior is that when your throwing lambda throws a checked exception, a ThrownByLambdaException is thrown with the checked exception as the cause. You can therefore capture that and get the cause.
Other features are available as well.
There are a lot of great responses already posted here. Just attempting to solve the problem with a different perspective. Its just my 2 cents, please correct me if I am wrong somewhere.
Throws clause in FunctionalInterface is not a good idea
I think this is probably not a good idea to enforce throws IOException because of following reasons
This looks to me like an anti-pattern to Stream/Lambda. The whole idea is that the caller will decide what code to provide and how to handle the exception. In many scenarios, the IOException might not be applicable for the client. For example, if the client is getting value from cache/memory instead of performing actual I/O.
Also, the exceptions handling in streams becomes really hideous. For example, here is my code will look like if I use your API
acceptMyMethod(s -> {
try {
Integer i = doSomeOperation(s);
return i;
} catch (IOException e) {
// try catch block because of throws clause
// in functional method, even though doSomeOperation
// might not be throwing any exception at all.
e.printStackTrace();
}
return null;
});
Ugly isn't it? Moreover, as I mentioned in my first point, that the doSomeOperation method may or may not be throwing IOException (depending on the implementation of the client/caller), but because of the throws clause in your FunctionalInterface method, I always have to write the try-catch.
What do I do if I really know this API throws IOException
Then probably we are confusing FunctionalInterface with typical Interfaces. If you know this API will throw IOException, then most probably you also know some default/abstract behavior as well. I think you should define an interface and deploy your library (with default/abstract implementation) as follows
public interface MyAmazingAPI {
Integer myMethod(String s) throws IOException;
}
But, the try-catch problem still exists for the client. If I use your API in stream, I still need to handle IOException in hideous try-catch block.
Provide a default stream-friendly API as follows
public interface MyAmazingAPI {
Integer myMethod(String s) throws IOException;
default Optional<Integer> myMethod(String s, Consumer<? super Exception> exceptionConsumer) {
try {
return Optional.ofNullable(this.myMethod(s));
} catch (Exception e) {
if (exceptionConsumer != null) {
exceptionConsumer.accept(e);
} else {
e.printStackTrace();
}
}
return Optional.empty();
}
}
The default method takes the consumer object as argument, which will be responsible to handle the exception. Now, from client's point of view, the code will look like this
strStream.map(str -> amazingAPIs.myMethod(str, Exception::printStackTrace))
.filter(Optional::isPresent)
.map(Optional::get).collect(toList());
Nice right? Of course, logger or other handling logic could be used instead of Exception::printStackTrace.
You can also expose a method similar to https://docs.oracle.com/javase/8/docs/api/java/util/concurrent/CompletableFuture.html#exceptionally-java.util.function.Function- . Meaning that you can expose another method, which will contain the exception from previous method call. The disadvantage is that you are now making your APIs stateful, which means that you need to handle thread-safety and which will be eventually become a performance hit. Just an option to consider though.
By default, Java 8 Function does not allow to throw exception and as suggested in multiple answers there are many ways to achieve it, one way is:
#FunctionalInterface
public interface FunctionWithException<T, R, E extends Exception> {
R apply(T t) throws E;
}
Define as:
private FunctionWithException<String, Integer, IOException> myMethod = (str) -> {
if ("abc".equals(str)) {
throw new IOException();
}
return 1;
};
And add throws or try/catch the same exception in caller method.
I use an overloaded utility function called unchecked() which handles multiple use-cases.
SOME EAMPLE USAGES
unchecked(() -> new File("hello.txt").createNewFile());
boolean fileWasCreated = unchecked(() -> new File("hello.txt").createNewFile());
myFiles.forEach(unchecked(file -> new File(file.path).createNewFile()));
SUPPORTING UTILITIES
public class UncheckedUtils {
#FunctionalInterface
public interface ThrowingConsumer<T> {
void accept(T t) throws Exception;
}
#FunctionalInterface
public interface ThrowingSupplier<T> {
T get() throws Exception;
}
#FunctionalInterface
public interface ThrowingRunnable {
void run() throws Exception;
}
public static <T> Consumer<T> unchecked(
ThrowingConsumer<T> throwingConsumer
) {
return i -> {
try {
throwingConsumer.accept(i);
} catch (Exception ex) {
throw new RuntimeException(ex);
}
};
}
public static <T> T unchecked(
ThrowingSupplier<T> throwingSupplier
) {
try {
return throwingSupplier.get();
} catch (Exception ex) {
throw new RuntimeException(ex);
}
}
public static void unchecked(
ThrowingRunnable throwing
) {
try {
throwing.run();
} catch (Exception ex) {
throw new RuntimeException(ex);
}
}
}
You can use ET for this. ET is a small Java 8 library for exception conversion/translation.
With ET it looks like this:
// Do this once
ExceptionTranslator et = ET.newConfiguration().done();
...
// if your method returns something
Function<String, Integer> f = (t) -> et.withReturningTranslation(() -> myMethod(t));
// if your method returns nothing
Consumer<String> c = (t) -> et.withTranslation(() -> myMethod(t));
ExceptionTranslator instances are thread safe an can be shared by multiple components. You can configure more specific exception conversion rules (e.g. FooCheckedException -> BarRuntimeException) if you like.
If no other rules are available, checked exceptions are automatically converted to RuntimeException.
(Disclaimer: I am the author of ET)
If you don't mind using a third party library, with cyclops-react, a library I contribute to, you can use the FluentFunctions API to write
Function<String, Integer> standardFn = FluentFunctions.ofChecked(this::myMethod);
ofChecked takes a jOOλ CheckedFunction and returns the reference softened back to a standard (unchecked) JDK java.util.function.Function.
Alternatively you can keep working with the captured function via the FluentFunctions api!
For example to execute your method, retrying it up to 5 times and logging it's status you can write
FluentFunctions.ofChecked(this::myMethod)
.log(s->log.debug(s),e->log.error(e,e.getMessage())
.try(5,1000)
.apply("my param");
What I'm doing is to allow the user to give the value he actually want in case of exception .
So I've something looking like this
public static <T, R> Function<? super T, ? extends R> defaultIfThrows(FunctionThatThrows<? super T, ? extends R> delegate, R defaultValue) {
return x -> {
try {
return delegate.apply(x);
} catch (Throwable throwable) {
return defaultValue;
}
};
}
#FunctionalInterface
public interface FunctionThatThrows<T, R> {
R apply(T t) throws Throwable;
}
And this can then be call like :
defaultIfThrows(child -> child.getID(), null)
Use Jool Library or say jOOλ library from JOOQ. It not only provides unchecked exception handled interfaces but also provides Seq class with lots of useful methods.
Also, it contains Functional Interfaces with up to 16 parameters. Also, it provides Tuple class which is used in different scenarios.
Jool Git Link
Specifically in library lookup for org.jooq.lambda.fi.util.function package. It contains all the Interfaces from Java-8 with Checked prepended. See below for reference:-
If you have lombok, you can annotate your method with #SneakyThrows
SneakyThrow does not silently swallow, wrap into RuntimeException, or otherwise modify any exceptions of the listed checked exception types. The JVM does not check for the consistency of the checked exception system; javac does, and this annotation lets you opt out of its mechanism.
https://projectlombok.org/features/SneakyThrows
Several of the offered solutions use a generic argument of E to pass in the type of the exception which gets thrown.
Take that one step further, and rather than passing in the type of the exception, pass in a Consumer of the type of exception, as in...
Consumer<E extends Exception>
You might create several re-usable variations of Consumer<Exception> which would cover the common exception handling needs of your application.
I will do something generic:
public interface Lambda {
#FunctionalInterface
public interface CheckedFunction<T> {
T get() throws Exception;
}
public static <T> T handle(CheckedFunction<T> supplier) {
try {
return supplier.get();
} catch (Exception exception) {
throw new RuntimeException(exception);
}
}
}
usage:
Lambda.handle(() -> method());
I'm the author of a tiny lib with some generic magic to throw any Java Exception anywhere without the need of catching them nor wrapping them into RuntimeException.
Usage:
unchecked(() -> methodThrowingCheckedException())
public class UncheckedExceptions {
/**
* throws {#code exception} as unchecked exception, without wrapping exception.
*
* #return will never return anything, return type is set to {#code exception} only to be able to write <code>throw unchecked(exception)</code>
* #throws T {#code exception} as unchecked exception
*/
#SuppressWarnings("unchecked")
public static <T extends Throwable> T unchecked(Exception exception) throws T {
throw (T) exception;
}
#FunctionalInterface
public interface UncheckedFunction<R> {
R call() throws Exception;
}
/**
* Executes given function,
* catches and rethrows checked exceptions as unchecked exceptions, without wrapping exception.
*
* #return result of function
* #see #unchecked(Exception)
*/
public static <R> R unchecked(UncheckedFunction<R> function) {
try {
return function.call();
} catch (Exception e) {
throw unchecked(e);
}
}
#FunctionalInterface
public interface UncheckedMethod {
void call() throws Exception;
}
/**
* Executes given method,
* catches and rethrows checked exceptions as unchecked exceptions, without wrapping exception.
*
* #see #unchecked(Exception)
*/
public static void unchecked(UncheckedMethod method) {
try {
method.call();
} catch (Exception e) {
throw unchecked(e);
}
}
}
source: https://github.com/qoomon/unchecked-exceptions-java
For me the preferred solution is to use Lombok. It is a nice library anyway.
Instead of:
Integer myMethod(String s) throws IOException
you will have
import lombok.SneakyThrows;
#SneakyThrows
Integer myMethod(String s)
The exception is still thrown but you do not need to declare it with throws.
public void frankTest() {
int pageId= -1;
List<Book> users= null;
try {
//Does Not Compile: Object page=DatabaseConnection.getSpringConnection().queryForObject("SELECT * FROM bookmark_page", (rw, n) -> new Portal(rw.getInt("id"), "", users.parallelStream().filter(uu -> uu.getVbid() == rw.getString("user_id")).findFirst().get(), rw.getString("name")));
//Compiles:
Object page= DatabaseConnection.getSpringConnection().queryForObject("SELECT * FROM bookmark_page", (rw, n) -> {
try {
final Book bk= users.stream().filter(bp -> {
String name= null;
try {
name = rw.getString("name");
} catch (Exception e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
return bp.getTitle().equals(name);
}).limit(1).collect(Collectors.toList()).get(0);
} catch (Exception e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
return new Portal(rw.getInt("id"), "", users.get(0), rw.getString("name"));
} );
} catch (Exception e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}

classPool.get(className) throws RuntimeException cannot find class

I am trying to write a simple instrumentation agent using Javassist.
public class Agent implements ClassFileTransformer {
protected Instrumentation instrumentation;
protected ClassPool classPool;
public Agent(Instrumentation instrumentation){
this.instrumentation = instrumentation;
this.classPool = ClassPool.getDefault();
this.instrumentation.addTransformer(this);
}
public byte[] transform(ClassLoader loader, String className, Class<?> classBeingRedefined, ProtectionDomain protectionDomain, byte[] classfileBuffer) throws IllegalClassFormatException {
try {
System.out.printf("%s.transform: %s\n", this.getClass().getCanonicalName(), className);
classPool.insertClassPath(new ByteArrayClassPath(className, classfileBuffer));
CtClass ctClass = classPool.get(className); /* <- throws error */
}
catch (Exception ex){
System.out.println(ex);
return null;
}
}
}
But I get the following errors:
java.lang.RuntimeException: cannot find java/lang/invoke/MethodHandleImpl: java.lang.invoke.MethodHandleImpl found in java/lang/invoke/MethodHandleImpl.class
The only class that doesn't throw this exception is the one in my project in the IDE (IntelliJ IDEA).
I tried to add the paths from the classpath manually, but that didn't help either. i.e.
String[] cpEntries = System.getProperty("java.class.path").split(File.pathSeparator);
for (String cpEntry : classpathEntries)
classPool.insertClassPath(cpEntry);
What am I missing? Thanks!
The problem is that className's separator is a /, while classPool.get(className) expects the . delimiter, so the fix is to replace those characters, i.e.:
String classNameDotted = className.replace('/', '.');
CtClass ctClass = classPool.get(classNameDotted);

Is there a way to make a custom implementation of Nashorn JSObject work with Object.keys()?

I recently asked this question How can I pass a proper method reference in so Nashorn can execute it? and got an answer that helped me get much further along with my project, but I discovered a limitation around providing a custom JSObject implementation that I don't know how to resolve.
Given this simple working JSObject that can handle most of the methods JS would invoke on it such as map:
import javax.script.*;
import jdk.nashorn.api.scripting.*;
import java.util.*;
import java.util.function.*;
public class scratch_6 {
public static void main(String[] args) throws Exception {
ScriptEngineManager m = new ScriptEngineManager();
ScriptEngine e = m.getEngineByName("nashorn");
// The following JSObject wraps this list
List<Object> l = new ArrayList<>();
l.add("hello");
l.add("world");
l.add(true);
l.add(1);
JSObject jsObj = new AbstractJSObject() {
#Override
public Object getMember(String name) {
if (name.equals("map")) {
// return a functional interface object - nashorn will treat it like
// script function!
final Function<JSObject, Object> jsObjectObjectFunction = callback -> {
List<Object> res = new ArrayList<>();
for (Object obj : l) {
// call callback on each object and add the result to new list
res.add(callback.call(null, obj));
}
// return fresh list as result of map (or this could be another wrapper)
return res;
};
return jsObjectObjectFunction;
} else {
// unknown property
return null;
}
}
};
e.put("obj", jsObj);
// map each String to it's uppercase and print result of map
e.eval("print(obj.map(function(x) '\"'+x.toString()+'\"'))");
//PROBLEM
//e.eval("print(Object.keys(obj))");
}
}
If you uncomment the last line where Object.keys(obj) is called, it will fail with the error ... is not an Object.
This appears to be because Object.keys() [ NativeObject.java:376 ] only checks whether the object is an instance of ScriptObject or of ScriptObjectMirror. If it is neither of those things, it throws the notAnObject error. :(
Ideally, user implemented JSObject objects should be exactly equivalent to script objects. But, user implemented JSObjects are almost script objects - but not quite. This is documented here -> https://wiki.openjdk.java.net/display/Nashorn/Nashorn+jsr223+engine+notes
Object.keys is one such case where it breaks. However, if you just want for..in javascript iteration support for your objects, you can implement JSObject.keySet in your class.
Example code:
import javax.script.*;
import jdk.nashorn.api.scripting.*;
import java.util.*;
public class Main {
public static void main(String[] args) throws Exception {
ScriptEngineManager m = new ScriptEngineManager();
ScriptEngine e = m.getEngineByName("nashorn");
// This JSObject wraps the following Properties object
Properties props = System.getProperties();
JSObject jsObj = new AbstractJSObject() {
#Override
public Set<String> keySet() {
return props.stringPropertyNames();
}
#Override
public Object getMember(String name) {
return props.getProperty(name);
}
};
e.put("obj", jsObj);
e.eval("for (i in obj) print(i, ' = ', obj[i])");
}
}

biojava Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException:

I have problem with multiple sequence alignement. I have two sequences as follow and I m trying to align them using biojava methods and I get error like this. I have no idea what is wrong. I know that sequences are not the same length but it should not matter.
GSKTGTKITFYEDKNFQGRRYDCDCDCADFHTYLSRCNSIKVEGGTWAVYERPNFAGYMYILPQGEYPEYQRWMGLNDRLSSCRAVHLPSGGQYKIQIFEKGDFSGQMYETTEDCPSIMEQFHMREIHSCKVLEGVWIFYELPNYRGRQYLLDKKEYRKPIDWGAASPAVQSFRRIVE
SMSAGPWKMVVWDEDGFQGRRHEFTAECPSVLELGFETVRSLKVLSGAWVGFEHAGFQGQQYILERGEYPSWDAWGGNTAYPAERLTSFRPAACANHRDSRLTIFEQENFLGKKGELSDDYPSLQAMGWEGNEVGSFHVHSGAWVCSQFPGYRGFQYVLECDHHSGDYKHFREWGSHAPTFQVQSIRRIQQ
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 1
at
org.forester.evoinference.distance.NeighborJoining.getValueFromD(NeighborJoining.java:150)
at
org.forester.evoinference.distance.NeighborJoining.execute(NeighborJoining.java:123)
at org.biojava3.alignment.GuideTree.(GuideTree.java:88) at
org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:183)
at Fasta.main(Fasta.java:41)
public class Fasta {
public static void main(String[] args) throws Exception{
ArrayList<String> fileName = new ArrayList<String> ();
fileName.add("2M3T.fasta.txt");
fileName.add("3LWK.fasta.txt");
ArrayList<ProteinSequence> al = new ArrayList<ProteinSequence>();
//ArrayList<ProteinSequence> all = new ArrayList<ProteinSequence>();
for (String fn : fileName)
{
al = getProteinSequenceFromFasta(fn);
//all.add(al.get(0));
for (ProteinSequence s : al)
{
System.out.println(s);
}
}
Profile<ProteinSequence, AminoAcidCompound> profile = Alignments.getMultipleSequenceAlignment(al);
System.out.printf("Clustalw:%n%s%n", profile);
ConcurrencyTools.shutdown();
}
//for (int i=0;i<sequence.size();i++)
// System.out.println(sequence);
public static ArrayList<ProteinSequence> getProteinSequenceFromFasta(String file) throws Exception{
LinkedHashMap<String, ProteinSequence> a = FastaReaderHelper.readFastaProteinSequence(new File(file));
//sztuczne
ArrayList<ProteinSequence> sequence = new ArrayList<ProteinSequence>(a.values());
return sequence;
}
}
My guess is the problem is at this line:
for (String fn : fileName)
{
al = getProteinSequenceFromFasta(fn);
...
}
You are overwriting the contents of a1 for each file. (I assume you want to add all the fasta records into a1. If your fasta files only has 1 record each then it can't do a multiple alignment to a single record.
You probably want
for (String fn : fileName)
{
al.addAll(getProteinSequenceFromFasta(fn) );
...
}
Granted, the library you are using should probably have checked first to make sure there are more than 1 sequences....

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