Apologies if this an old topic, however the following test program:

package com.viavi;

import org.apache.hadoop.fs.FsUrlStreamHandlerFactory;

import java.io.File;
import java.net.MalformedURLException;
import java.net.URI;
import java.net.URISyntaxException;
import java.net.URL;

public class Main {

    public static void main(String[] args) {
        System.out.println("URI is " + makeURI());
        URL.setURLStreamHandlerFactory(new FsUrlStreamHandlerFactory());
        System.out.println("URI is " + makeURI());
    }

    private static URI makeURI() {
        try {
            File file = new File("C:/Users");
            final URL url = new URL("file:///" + file.getAbsolutePath());
            return url.toURI();
        } catch (MalformedURLException x) {
            x.printStackTrace();
            return null;
        } catch (URISyntaxException x) {
            x.printStackTrace();
            return null;
        }
    }
}

gives the following output:

URI is file:/C:/Users
URI is null
java.net.URISyntaxException: Illegal character in path at index 8: 
file:/C:\Users
                at java.net.URI$Parser.fail(URI.java:2848)
                at java.net.URI$Parser.checkChars(URI.java:3021)
                at java.net.URI$Parser.parseHierarchical(URI.java:3105)
                at java.net.URI$Parser.parse(URI.java:3053)
                at java.net.URI.<init>(URI.java:588)
                at java.net.URL.toURI(URL.java:946)
                at com.viavi.Main.makeURI(Main.java:23)
                at com.viavi.Main.main(Main.java:16)
                at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
                at 
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
                at 
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
                at java.lang.reflect.Method.invoke(Method.java:498)
                at 
com.intellij.rt.execution.application.AppMain.main(AppMain.java:147)

That is, it seems that registering the FsUrlStreamHandlerFactory disrupts the 
subsequent creation of Windows "file" URLs.
I encountered this on 2.6.5, and have reproduced in 3.0.0 - alpha2.

I believe I have a fair understanding of the root of the issue. Is this of 
interest to anybody?

Thanks
Simon

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