4Quant · kmader · Dec 5, 2014 · Oct 7, 2014 · Oct 7, 2014 · Oct 8, 2014
diff --git a/pom.xml b/pom.xml
@@ -5,12 +5,12 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>3.6</version>
+		<version>5.1</version>
 		<relativePath />
 	</parent>
 
 	<artifactId>scijava-common</artifactId>
-	<version>2.33.1-SNAPSHOT</version>
+	<version>2.35.2-SNAPSHOT</version>
 
 	<name>SciJava Common</name>
 	<description>SciJava Common is a shared library for SciJava software. It provides a plugin framework, with an extensible mechanism for service discovery, backed by its own annotation processor, so that plugins can be loaded dynamically. It is used by both ImageJ and SCIFIO.</description>

diff --git a/src/main/java/org/scijava/AbstractUIDetails.java b/src/main/java/org/scijava/AbstractUIDetails.java
@@ -105,7 +105,8 @@ public String getTitle() {
 
 		// use the unique identifier, if available
 		if (this instanceof Identifiable) {
-			return ((Identifiable) this).getIdentifier();
+			final String id = ((Identifiable) this).getIdentifier();
+			if (id != null) return id;
 		}
 
 		// use class name as a last resort
@@ -235,7 +236,7 @@ public int compareTo(final Prioritized that) {
 		// compare titles
 		final String thisTitle = getTitle();
 		final String thatTitle = uiDetails.getTitle();
-		return thisTitle.compareTo(thatTitle);
+		return MiscUtils.compare(thisTitle, thatTitle);
 	}
 
 }
diff --git a/src/main/java/org/scijava/annotations/AbstractIndexWriter.java b/src/main/java/org/scijava/annotations/AbstractIndexWriter.java
@@ -45,6 +45,8 @@
 import java.util.Map.Entry;
 import java.util.TreeMap;
 
+import javax.lang.model.element.AnnotationValue;
+
 /**
  * Writes annotations as JSON-formatted files.
  * <p>
@@ -170,6 +172,9 @@ protected Object adapt(final Object o) {
 		if (o instanceof Annotation) {
 			return adapt((Annotation) o);
 		}
+		else if (o instanceof AnnotationValue) {
+			return adapt(((AnnotationValue) o).getValue());
+		}
 		else if (o instanceof Enum) {
 			return adapt((Enum<?>) o);
 		}

diff --git a/src/main/java/org/scijava/annotations/AnnotationProcessor.java b/src/main/java/org/scijava/annotations/AnnotationProcessor.java
@@ -32,7 +32,9 @@
 package org.scijava.annotations;
 
 import java.io.ByteArrayOutputStream;
+import java.io.File;
 import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
@@ -62,6 +64,7 @@
 import javax.lang.model.util.Elements;
 import javax.lang.model.util.Types;
 import javax.tools.Diagnostic.Kind;
+import javax.tools.FileObject;
 import javax.tools.StandardLocation;
 
 import org.scijava.annotations.AbstractIndexWriter.StreamFactory;
@@ -90,14 +93,14 @@ public boolean process(final Set<? extends TypeElement> elements,
 		try {
 			writer.write(writer);
 		}
-		catch (IOException e) {
+		catch (final IOException e) {
 			final ByteArrayOutputStream out = new ByteArrayOutputStream();
 			e.printStackTrace(new PrintStream(out));
 			try {
 				out.close();
 				processingEnv.getMessager().printMessage(Kind.ERROR, out.toString());
 			}
-			catch (IOException e2) {
+			catch (final IOException e2) {
 				processingEnv.getMessager().printMessage(Kind.ERROR,
 					e2.getMessage() + " while printing " + e.getMessage());
 			}
@@ -152,8 +155,9 @@ public void add(final TypeElement element) {
 		}
 
 		@SuppressWarnings("unchecked")
-		private Map<String, Object> adapt(List<? extends AnnotationMirror> mirrors,
-			TypeMirror annotationType)
+		private Map<String, Object> adapt(
+			final List<? extends AnnotationMirror> mirrors,
+			final TypeMirror annotationType)
 		{
 			final Map<String, Object> result = new TreeMap<String, Object>();
 			for (final AnnotationMirror mirror : mirrors) {
@@ -208,7 +212,8 @@ else if (o instanceof VariableElement) {
 		}
 
 		private AnnotationMirror getMirror(final TypeElement element) {
-			for (AnnotationMirror candidate : utils.getAllAnnotationMirrors(element))
+			for (final AnnotationMirror candidate : utils
+				.getAllAnnotationMirrors(element))
 			{
 				final Name binaryName =
 					utils.getBinaryName((TypeElement) candidate.getAnnotationType()
@@ -221,7 +226,9 @@ private AnnotationMirror getMirror(final TypeElement element) {
 		}
 
 		@Override
-		public InputStream openInput(String annotationName) throws IOException {
+		public InputStream openInput(final String annotationName)
+			throws IOException
+		{
 			try {
 				return filer.getResource(StandardLocation.CLASS_OUTPUT, "",
 					Index.INDEX_PREFIX + annotationName).openInputStream();
@@ -232,16 +239,37 @@ public InputStream openInput(String annotationName) throws IOException {
 		}
 
 		@Override
-		public OutputStream openOutput(String annotationName) throws IOException {
+		public OutputStream openOutput(final String annotationName)
+			throws IOException
+		{
 			final List<Element> originating = originatingElements.get(annotationName);
-			return filer.createResource(StandardLocation.CLASS_OUTPUT, "",
-				Index.INDEX_PREFIX + annotationName,
-				originating.toArray(new Element[originating.size()]))
-				.openOutputStream();
+			final String path = Index.INDEX_PREFIX + annotationName;
+			final FileObject fileObject =
+				filer.createResource(StandardLocation.CLASS_OUTPUT, "", path,
+					originating.toArray(new Element[originating.size()]));
+
+			/*
+			 * Verify that the generated file is in the META-INF/json/ subdirectory;
+			 * Despite our asking for it explicitly, the DefaultFileManager will
+			 * strip out the directory if javac was called without an explicit
+			 * output directory (i.e. without <code>-d</code> option).
+			 */
+			final String uri = fileObject.toUri().toString();
+			if (uri != null && uri.endsWith("/" + path)) {
+				return fileObject.openOutputStream();
+			}
+			final String prefix =
+				uri.substring(0, uri.length() - annotationName.length());
+			final File file = new File(prefix + path);
+			final File parent = file.getParentFile();
+			if (parent != null && !parent.isDirectory() && !parent.mkdirs()) {
+				throw new IOException("Could not create directory: " + parent);
+			}
+			return new FileOutputStream(file);
 		}
 
 		@Override
-		public boolean isClassObsolete(String className) {
+		public boolean isClassObsolete(final String className) {
 			return false;
 		}
 

diff --git a/src/main/java/org/scijava/menu/ShadowMenu.java b/src/main/java/org/scijava/menu/ShadowMenu.java
@@ -529,14 +529,15 @@ private ShadowMenu addChild(final ModuleInfo info, final int depth) {
 		if (!leaf) child.addChild(info, depth + 1);
 		else if (existingChild != null) {
 			if (log != null) {
-				if (info.getPriority() == existingChild.getModuleInfo().getPriority()) {
+				final ModuleInfo childInfo = existingChild.getModuleInfo();
+				if (childInfo != null && info.getPriority() == childInfo.getPriority())
+				{
 					log.warn("ShadowMenu: menu item already exists:\n\texisting: " +
-						existingChild.getModuleInfo() + "\n\t ignored: " + info);
+						childInfo + "\n\t ignored: " + info);
 				}
 				else {
 					log.debug("ShadowMenu: higher-priority menu item already exists:\n" +
-						"\texisting: " + existingChild.getModuleInfo() + "\n\t ignored: " +
-						info);
+						"\texisting: " + childInfo + "\n\t ignored: " + info);
 				}
 			}
 		}

diff --git a/src/main/java/org/scijava/prefs/DefaultPrefService.java b/src/main/java/org/scijava/prefs/DefaultPrefService.java
@@ -378,6 +378,28 @@ public List<String> getList(final Class<?> prefClass) {
 		return getList(preferences);
 	}
 
+	@Override
+	public Iterable<String> getIterable(final String key) {
+		return getIterable((Class<?>) null, key);
+	}
+
+	@Override
+	public Iterable<String> getIterable(final Class<?> prefClass, final String key) {
+		final Preferences preferences = prefs(prefClass);
+		return getIterable(preferences.node(key));
+	}
+
+	@Override
+	public void putIterable(final Iterable<String> iterable, final String key) {
+		putIterable((Class<?>) null, iterable, key);
+	}
+
+	@Override
+	public void putIterable(final Class<?> prefClass, final Iterable<String> iterable, final String key) {
+		final Preferences preferences = prefs(prefClass);
+		putIterable(preferences.node(key), iterable);
+	}
+
 	// -- Helper methods --
 
 	private void clear(final Preferences preferences, final String key) {
@@ -460,6 +482,60 @@ private List<String> getList(final Preferences preferences) {
 		return list;
 	}
 
+	private void putIterable(final Preferences preferences,
+		final Iterable<String> iterable)
+	{
+		if (preferences == null) {
+			throw new IllegalArgumentException("Preferences not set.");
+		}
+		int index = 0;
+		for (final String value : iterable) {
+			preferences.put("" + index++, value == null ? null : value.toString());
+		}
+	}
+
+	private Iterable<String> getIterable(final Preferences preferences)
+	{
+		if (preferences == null) {
+			throw new IllegalArgumentException("Preferences not set.");
+		}
+		return new Iterable<String>() {
+			@Override
+			public Iterator<String> iterator() {
+				return new Iterator<String>() {
+					private String value;
+					private int index;
+					{
+						findNext();
+					}
+
+					@Override
+					public String next() {
+						final String result = value;
+						findNext();
+						return result;
+					}
+
+					@Override
+					public boolean hasNext() {
+						return value != null;
+					}
+
+					@Override
+					public void remove() {
+						throw new UnsupportedOperationException();
+					}
+
+					private void findNext() {
+						if (index < 0) return;
+						value = preferences.get("" + index, null);
+						index = value == null ? -1 : index + 1;
+					}
+				};
+			}
+		};
+	}
+
 	private Preferences prefs(final Class<?> c) {
 		return Preferences.userNodeForPackage(c == null ? PrefService.class : c);
 	}

diff --git a/src/main/java/org/scijava/prefs/PrefService.java b/src/main/java/org/scijava/prefs/PrefService.java
@@ -194,4 +194,24 @@ public interface PrefService extends SciJavaService {
 	 * prefs.
 	 */
 	List<String> getList(Class<?> prefClass);
+
+	/**
+	 * Puts an iterable into the preferences.
+	 */
+	void putIterable(Iterable<String> iterable, String key);
+
+	/**
+	 * Puts an iterable into the preferences.
+	 */
+	void putIterable(Class<?> prefClass, Iterable<String> iterable, String key);
+
+	/**
+	 * Gets an iterable from the preferences.
+	 */
+	Iterable<String> getIterable(String key);
+
+	/**
+	 * Gets an iterable from the preferences.
+	 */
+	Iterable<String> getIterable(Class<?> prefClass, String key);
 }