URI and Path specifier classes for input/output resources. (#34)

Merging an initial but contested proposal in order to have something  concrete we can work on.

* URI and Path specifier classes for input/output resources.

* Changes for Windows and test refactoring.

build.gradle

@@ -30,6 +30,10 @@ subprojects {
 
     dependencies {
         testCompile "org.testng:testng:6.14.3"
+        testCompile "com.google.jimfs:jimfs:1.1"
+        testCompile "org.apache.commons:commons-lang3:3.7"
+
+        compile 'commons-io:commons-io:2.5'
     }
 
     test {

core/-

@@ -0,0 +1 @@
+some stuff

core/src/main/java/org/htsjdk/core/api/io/IOResource.java

@@ -0,0 +1,90 @@
+package org.htsjdk.core.api.io;
+
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.net.URI;
+import java.nio.file.Path;
+import java.util.Optional;
+
+/**
+ * Interface representing htsjdk-next input/output resources.
+ */
+public interface IOResource {
+
+    /**
+     * Determine if this resource has a scheme that has an installed NIO file system provider. This does not
+     * guarantee the resource can be converted into a {@code java.nio.file.Path}, since the resource can be
+     * syntactically valid, and specify a valid file system provider, but still fail to be semantically meaningful.
+     * @return true if this URI has a scheme that has an installed NIO file system provider.
+     */
+    boolean isNIO();
+
+    /**
+     * Return true if this {code IOResource} can be resolved to an NIO Path. If true, {@code #toPath()} can be
+     * safely called.
+     *
+     * There are cases where a valid URI with a valid scheme backed by an installed NIO File System
+     * still can't be turned into a {@code java.nio.file.Path}, i.e., the following specifies an invalid
+     * authority "namenode":
+     *
+     *  file://namenode/to/file
+     *
+     * @return {@code true} if this {@code IOResource} can be resolved to an NIO Path.
+     */
+    boolean isPath();
+
+    /**
+     * Get a {@code java.net.URI} object for this {@code IOResource}. Will not be null.
+     * @return The {@code URI} object for this IOResource.
+     */
+    URI getURI();
+
+    /**
+     * Returns the String representation of the {{@code UR} backing this {@code IOResource} URI. This string
+     * may differ from the normalized string returned from a Path that has been object resolved from this
+     * IOResource.
+     *
+     * @return String from which this URI as originally created. Will not be null, and will always
+     * include a URI scheme.
+     */
+    default String getURIString() { return getURI().toString(); }
+
+    /**
+     * Return the raw (source) input used to create this {@code IOResource} as a String.
+     */
+    String getRawInputString();
+
+    /**
+     * Resolve this {@code IOResource} to an NIO Path. Can be safely called only if {@link #isPath()} returns true.
+     */
+    Path toPath();
+
+    /**
+     * Return a string message describing why this IOResource cannot be converted to a {@code java.nio.file.Path}
+     * ({@code #isPath()} returns false).
+     *
+     * @return Optional<String></String> message explaining toPath failure reason, since it can fail for various reasons.
+     */
+    Optional<String> getToPathFailureReason();
+
+    /**
+     * Return the scheme for this IOResource. For file resources (URIs that have no explicit scheme), this
+     * will return the scheme "file".
+     * @return the scheme String for the URI backing this {@code IOResource}, if any. Will not be  null.
+     */
+    default String getScheme() {
+        return getURI().getScheme();
+    }
+
+    /**
+     * Get a {@code InputStream} for this resource.
+     * @return {@code InputStream} for this resource.
+     */
+    InputStream getInputStream();
+
+    /**
+     * Get an {@code OutputStream} for this resource.
+     * @return {@code OutputStream} for this URI.
+     */
+    OutputStream getOutputStream();
+}

core/src/main/java/org/htsjdk/core/exception/HtsjdkIOException.java

@@ -0,0 +1,32 @@
+package org.htsjdk.core.exception;
+
+public class HtsjdkIOException extends HtsjdkException {
+
+    /**
+     * Constructs an HtsjdkIOException exception.
+     *
+     * @param message detailed message.
+     */
+    public HtsjdkIOException(String message) {
+        super(message);
+    }
+
+    /**
+     * Constructs an HtsjdkIOException exception with a specified cause.
+     *
+     * @param message detailed message.
+     * @param cause   cause of the exception.
+     */
+    public HtsjdkIOException(String message, Throwable cause) {
+        super(message, cause);
+    }
+
+    /**
+     * Constructs an HtsjdkIOException exception with a message constructed from the cause.
+     *
+     * @param cause cause of the exception.
+     */
+    public HtsjdkIOException(Throwable cause) {
+        super(cause);
+    }
+}

core/src/main/java/org/htsjdk/core/utils/IOUtils.java

@@ -0,0 +1,22 @@
+package org.htsjdk.core.utils;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Path;
+
+public class IOUtils {
+
+    /**
+     * Create a temporary file using a given name prefix and name suffix and return a {@link java.nio.file.Path}.
+     * @param prefix
+     * @param suffix
+     * @return temp File that will be deleted on exit
+     * @throws IOException
+     */
+    public static Path createTempPath(final String prefix, final String suffix) throws IOException {
+        final File tempFile = File.createTempFile(prefix, suffix);
+        tempFile.deleteOnExit();
+        return tempFile.toPath();
+    }
+
+}