Add TypedIOService

This is an interface which can be used to write IOServices opening and
saving a specific type. The TypedIOServiceTest class demonstrates how to
do that with an exemplary TextIOService.

So far, IO services like DatasetIOService or TableIOServcie don't share
a common IOService interface.

src/main/java/org/scijava/io/AbstractTypedIOService.java

@@ -0,0 +1,140 @@
+/*
+ * #%L
+ * SciJava Common shared library for SciJava software.
+ * %%
+ * Copyright (C) 2009 - 2020 SciJava developers.
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+
+package org.scijava.io;
+
+import org.scijava.io.location.Location;
+import org.scijava.io.location.LocationService;
+import org.scijava.plugin.AbstractHandlerService;
+import org.scijava.plugin.Parameter;
+
+import java.io.IOException;
+import java.net.URISyntaxException;
+
+/**
+ * Abstract base class for typed {@link IOPlugin}s.
+ * 
+ * @author Curtis Rueden
+ * @author Deborah Schmidt
+ */
+public abstract class AbstractTypedIOService<D> extends AbstractHandlerService<Location, IOPlugin<D>> implements TypedIOService<D>
+{
+
+	@Parameter
+	private LocationService locationService;
+
+	@Parameter
+	private IOService ioService;
+
+	@Override
+	public D open(String source) throws IOException {
+		try {
+			return open(locationService.resolve(source));
+		} catch (URISyntaxException e) {
+			throw new IOException(e);
+		}
+	}
+
+	@Override
+	public D open(Location source) throws IOException {
+		IOPlugin<?> opener = ioService().getOpener(source);
+		try {
+			Class<D> ignored = (Class<D>) opener.getDataType();
+			return (D) opener.open(source);
+		}
+		catch(ClassCastException e) {
+			throw new UnsupportedOperationException("No compatible opener found.");
+		}
+	}
+
+	@Override
+	public void save(D data, String destination) throws IOException {
+		try {
+			save(data, locationService.resolve(destination));
+		} catch (URISyntaxException e) {
+			throw new IOException(e);
+		}
+	}
+
+	@Override
+	public void save(D data, Location destination) throws IOException {
+		IOPlugin<D> saver = ioService().getSaver(data, destination);
+		if (saver != null) {
+			saver.save(data, destination);
+		}
+		else {
+			throw new UnsupportedOperationException("No compatible saver found.");
+		}
+	}
+
+	@Override
+	public boolean canOpen(String source) {
+		try {
+			return canOpen(locationService.resolve(source));
+		} catch (URISyntaxException e) {
+			return false;
+		}
+	}
+
+	@Override
+	public boolean canOpen(Location source) {
+		IOPlugin<?> opener = ioService().getOpener(source);
+		if (opener == null) return false;
+		try {
+			Class<D> ignored = (Class<D>) (opener.getDataType());
+			return true;
+		} catch(ClassCastException e) {
+			return false;
+		}
+	}
+
+	@Override
+	public boolean canSave(D data, String source) {
+		try {
+			return canSave(data, locationService.resolve(source));
+		} catch (URISyntaxException e) {
+			return false;
+		}
+	}
+
+	@Override
+	public boolean canSave(D data, Location destination) {
+		IOPlugin<D> saver = ioService.getSaver(data, destination);
+		if (saver == null) return false;
+		return saver.supportsSave(destination);
+	}
+
+	protected LocationService locationService() {
+		return locationService;
+	}
+
+	protected IOService ioService() {
+		return ioService;
+	}
+}

src/main/java/org/scijava/io/TypedIOService.java

@@ -0,0 +1,168 @@
+/*
+ * #%L
+ * SciJava Common shared library for SciJava software.
+ * %%
+ * Copyright (C) 2009 - 2020 SciJava developers.
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+
+package org.scijava.io;
+
+import java.io.IOException;
+
+import org.scijava.io.location.FileLocation;
+import org.scijava.io.location.Location;
+import org.scijava.plugin.HandlerService;
+import org.scijava.service.SciJavaService;
+
+/**
+ * Interface for high-level data I/O: opening and saving data of a specific type.
+ *
+ * @author Curtis Rueden
+ * @author Deborah Schmidt
+ */
+public interface TypedIOService<D> extends HandlerService<Location, IOPlugin<D>>,
+		SciJavaService
+{
+
+	/**
+	 * Gets the most appropriate {@link IOPlugin} for opening data from the given
+	 * location.
+	 */
+	default IOPlugin<D> getOpener(final String source) {
+		return getOpener(new FileLocation(source));
+	}
+
+	/**
+	 * Gets the most appropriate {@link IOPlugin} for opening data from the given
+	 * location.
+	 */
+	default IOPlugin<D> getOpener(Location source) {
+		for (final IOPlugin<D> handler : getInstances()) {
+			if (handler.supportsOpen(source)) return handler;
+		}
+		return null;
+	}
+
+	/**
+	 * Gets the most appropriate {@link IOPlugin} for saving data to the given
+	 * location.
+	 */
+	default IOPlugin<D> getSaver(final D data, final String destination) {
+		return getSaver(data, new FileLocation(destination));
+	}
+
+	/**
+	 * Gets the most appropriate {@link IOPlugin} for saving data to the given
+	 * location.
+	 */
+	default IOPlugin<D> getSaver(D data, Location destination) {
+		for (final IOPlugin<?> handler : getInstances()) {
+			if (handler.supportsSave(data, destination)) {
+				return (IOPlugin<D>) handler;
+			}
+		}
+		return null;
+	}
+
+	/**
+	 * Loads data from the given source. For extensibility, the nature of the
+	 * source is left intentionally general, but two common examples include file
+	 * paths and URLs.
+	 * <p>
+	 * The opener to use is automatically determined based on available
+	 * {@link IOPlugin}s; see {@link #getOpener(String)}.
+	 * </p>
+	 *
+	 * @param source The source (e.g., file path) from which to data should be
+	 *          loaded.
+	 * @return An object representing the loaded data, or null if the source is
+	 *         not supported.
+	 * @throws IOException if something goes wrong loading the data.
+	 */
+	D open(String source) throws IOException;
+
+	/**
+	 * Loads data from the given location.
+	 * <p>
+	 * The opener to use is automatically determined based on available
+	 * {@link IOPlugin}s; see {@link #getOpener(Location)}.
+	 * </p>
+	 *
+	 * @param source The location from which to data should be loaded.
+	 * @return An object representing the loaded data, or null if the source is
+	 *         not supported.
+	 * @throws IOException if something goes wrong loading the data.
+	 */
+	D open(Location source) throws IOException;
+
+	/**
+	 * Saves data to the given destination. The nature of the destination is left
+	 * intentionally general, but the most common example is a file path.
+	 * <p>
+	 * The saver to use is automatically determined based on available
+	 * {@link IOPlugin}s; see {@link #getSaver(Object, String)}.
+	 * </p>
+	 *
+	 * @param data The data to be saved to the destination.
+	 * @param destination The destination (e.g., file path) to which data should
+	 *          be saved.
+	 * @throws IOException if something goes wrong saving the data.
+	 */
+	void save(D data, String destination) throws IOException;
+
+	/**
+	 * Saves data to the given location.
+	 * <p>
+	 * The saver to use is automatically determined based on available
+	 * {@link IOPlugin}s; see {@link #getSaver(Object, Location)}.
+	 * </p>
+	 *
+	 * @param data The data to be saved to the destination.
+	 * @param destination The destination location to which data should be saved.
+	 * @throws IOException if something goes wrong saving the data.
+	 */
+	void save(D data, Location destination) throws IOException;
+
+	boolean canOpen(String source);
+
+	boolean canOpen(Location source);
+
+	boolean canSave(D data, String destination);
+
+	boolean canSave(D data, Location destination);
+
+	// -- HandlerService methods --
+
+	@Override
+	@SuppressWarnings({ "rawtypes", "unchecked" })
+	default Class<IOPlugin<D>> getPluginType() {
+		return (Class) IOPlugin.class;
+	}
+
+	@Override
+	default Class<Location> getType() {
+		return Location.class;
+	}
+}

src/test/java/org/scijava/io/TypedIOServiceTest.java

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+package org.scijava.io;
+
+import org.junit.Test;
+import org.scijava.Context;
+import org.scijava.plugin.PluginInfo;
+import org.scijava.plugin.PluginService;
+import org.scijava.plugin.SciJavaPlugin;
+import org.scijava.service.SciJavaService;
+import org.scijava.text.AbstractTextFormat;
+import org.scijava.text.TextFormat;
+import org.scijava.text.TextService;
+
+import java.io.IOException;
+import java.util.Collections;
+import java.util.List;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+
+public class TypedIOServiceTest {
+
+	@Test
+	public void testTextFile() throws IOException {
+		// create context, add dummy text format
+		final Context ctx = new Context();
+		ctx.getPluginIndex().add(new PluginInfo<>(DummyTextFormat.class, TextFormat.class));
+		ctx.getPluginIndex().add(new PluginInfo<>(DefaultTextIOService.class, TextIOService.class));
+		TextIOService instance = (TextIOService) ctx.getService(PluginService.class).createInstance(ctx.getPluginIndex().get(TextIOService.class).get(0));
+		ctx.getServiceIndex().add(instance);
+
+		// try to get the TextIOService
+		final TextIOService io = ctx.service(TextIOService.class);
+		assertNotNull(io);
+
+		// open text file from resources as String
+		String localFile = getClass().getResource("test.txt").getPath();
+		String obj = io.open(localFile);
+		assertNotNull(obj);
+		assertTrue(obj.contains("content"));
+	}
+
+	interface TextIOService extends TypedIOService<String> {
+	}
+
+	public static class DefaultTextIOService extends AbstractTypedIOService<String> implements TextIOService {
+	}
+
+	public static class DummyTextFormat  extends AbstractTextFormat {
+
+		@Override
+		public List<String> getExtensions() {
+			return Collections.singletonList("txt");
+		}
+
+		@Override
+		public String asHTML(String text) {
+			return text;
+		}
+
+	}
+}