Merge branch 'recursive-injection'

This enhances the behavior of context injection to recursively inject
@Parameter-annotated fields when the field value is already assigned
to an object reference. This is especially useful for CommandModule,
which keeps a reference to its delegate Command instance. This Command
instance also needs the context injected at the same time it is injected
into the CommandModule instance. In the past, a couple of different
hacky solutions were employed, such as injecting the context into the
Command as part of initialize() -- but each hack had its limitations.
The best solution is to actually inject the context into member fields
at the same time it is injected into the base object itself.

This change ensures that Command instances always receive a context
injection immediately, even if e.g. no preprocessing is performed.

This branch is dedicated to Richard Domander.

Author: ctrueden

src/main/java/org/scijava/Context.java

@@ -471,6 +471,11 @@ else if (Context.class.isAssignableFrom(type) && type.isInstance(this)) {
 				// populate Context parameter
 				ClassUtils.setValue(f, o, this);
 			}
+			else if (!type.isPrimitive()) {
+				// the parameter is some other object; if it is non-null, we recurse
+				final Object value = ClassUtils.getValue(f, o);
+				if (value != null) inject(value);
+			}
 		}
 		catch (final Throwable t) {
 			handleSafely(t);
@@ -533,7 +538,6 @@ private static PluginIndex plugins(final boolean empty) {
 		return empty ? new PluginIndex(null) : null;
 	}
 
-	@SuppressWarnings("unchecked")
 	private static List<Class<? extends Service>> services(final boolean empty) {
 		if (empty) return Collections.<Class<? extends Service>> emptyList();
 		return Arrays.<Class<? extends Service>> asList(Service.class);

src/main/java/org/scijava/command/CommandModule.java

@@ -80,6 +80,7 @@ public class CommandModule extends AbstractModule implements Cancelable,
 	private final CommandInfo info;
 
 	/** The command instance handled by this module. */
+	@Parameter
 	private final Command command;
 
 	@Parameter

src/test/java/org/scijava/command/CommandModuleTest.java

@@ -34,6 +34,7 @@
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertSame;
 import static org.junit.Assert.assertTrue;
 
 import java.util.concurrent.ExecutionException;
@@ -112,6 +113,20 @@ public void testValidation() throws InterruptedException, ExecutionException {
 		assertEquals("success", module.getOutput("result"));
 	}
 
+	@Test
+	public void testCommandInjection() throws InterruptedException,
+		ExecutionException
+	{
+		final Context context = new Context(CommandService.class);
+		final CommandService commandService = context.service(CommandService.class);
+		final LogService logService = context.service(LogService.class);
+
+		final CommandModule module = //
+			commandService.run(CommandWithService.class, false).get();
+		assertSame(logService, module.getInput("log"));
+		assertTrue((boolean) module.getOutput("success"));
+	}
+
 	// -- Helper classes --
 
 	/** A command which implements {@link Cancelable}. */
@@ -235,4 +250,21 @@ public void process(final Module module) {
 
 	/** Placeholder class, for type safety. */
 	public static class Stuff {}
+
+	/** A command which has a {@link Service} parameter. */
+	@Plugin(type = Command.class)
+	public static class CommandWithService implements Command {
+
+		@Parameter
+		private LogService log;
+
+		@Parameter(type = ItemIO.OUTPUT)
+		private boolean success;
+
+		@Override
+		public void run() {
+			success = log != null;
+		}
+	}
+
 }