scijava · hinerm · Dec 20, 2013 · Dec 18, 2013 · Dec 18, 2013 · Dec 18, 2013
diff --git a/src/it/apt-test/pom.xml b/src/it/apt-test/pom.xml
@@ -1,9 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!--
   #%L
-  Annotation index (processor and index access library).
+  SciJava Common shared library for SciJava software.
   %%
-  Copyright (C) 2009 - 2013 Board of Regents of the University of Wisconsin-Madison.
+  Copyright (C) 2009 - 2013 Board of Regents of the University of
+  Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
+  Institute of Molecular Cell Biology and Genetics.
   %%
   Redistribution and use in source and binary forms, with or without
   modification, are permitted provided that the following conditions are met:

diff --git a/src/it/apt-test/src/main/java/org/scijava/annotation/its/Annotated.java b/src/it/apt-test/src/main/java/org/scijava/annotation/its/Annotated.java
@@ -1,8 +1,10 @@
 /*
  * #%L
- * Annotation index (processor and index access library).
+ * SciJava Common shared library for SciJava software.
  * %%
- * Copyright (C) 2009 - 2013 Board of Regents of the University of Wisconsin-Madison.
+ * Copyright (C) 2009 - 2013 Board of Regents of the University of
+ * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
+ * Institute of Molecular Cell Biology and Genetics.
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:

diff --git a/src/it/apt-test/src/main/java/org/scijava/annotation/its/CustomAnnotation.java b/src/it/apt-test/src/main/java/org/scijava/annotation/its/CustomAnnotation.java
@@ -1,8 +1,10 @@
 /*
  * #%L
- * Annotation index (processor and index access library).
+ * SciJava Common shared library for SciJava software.
  * %%
- * Copyright (C) 2009 - 2013 Board of Regents of the University of Wisconsin-Madison.
+ * Copyright (C) 2009 - 2013 Board of Regents of the University of
+ * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
+ * Institute of Molecular Cell Biology and Genetics.
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:

diff --git a/src/it/settings.xml b/src/it/settings.xml
@@ -1,9 +1,11 @@
 <?xml version="1.0"?>
 <!--
   #%L
-  Annotation index (processor and index access library).
+  SciJava Common shared library for SciJava software.
   %%
-  Copyright (C) 2009 - 2013 Board of Regents of the University of Wisconsin-Madison.
+  Copyright (C) 2009 - 2013 Board of Regents of the University of
+  Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
+  Institute of Molecular Cell Biology and Genetics.
   %%
   Redistribution and use in source and binary forms, with or without
   modification, are permitted provided that the following conditions are met:

diff --git a/src/main/java/org/scijava/Typed.java b/src/main/java/org/scijava/Typed.java
@@ -1,6 +1,6 @@
 /*
  * #%L
- * ImageJ software for multidimensional image processing and analysis.
+ * SciJava Common shared library for SciJava software.
  * %%
  * Copyright (C) 2009 - 2013 Board of Regents of the University of
  * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck

diff --git a/src/main/java/org/scijava/annotations/AbstractIndexWriter.java b/src/main/java/org/scijava/annotations/AbstractIndexWriter.java
@@ -1,8 +1,10 @@
 /*
  * #%L
- * Annotation index (processor and index access library).
+ * SciJava Common shared library for SciJava software.
  * %%
- * Copyright (C) 2009 - 2013 Board of Regents of the University of Wisconsin-Madison.
+ * Copyright (C) 2009 - 2013 Board of Regents of the University of
+ * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
+ * Institute of Molecular Cell Biology and Genetics.
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:

diff --git a/src/main/java/org/scijava/annotations/AnnotationCombiner.java b/src/main/java/org/scijava/annotations/AnnotationCombiner.java
@@ -0,0 +1,163 @@
+/*
+ * #%L
+ * SciJava Common shared library for SciJava software.
+ * %%
+ * Copyright (C) 2009 - 2013 Board of Regents of the University of
+ * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
+ * Institute of Molecular Cell Biology and Genetics.
+ * %%
+ * 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.
+ * 
+ * The views and conclusions contained in the software and documentation are
+ * those of the authors and should not be interpreted as representing official
+ * policies, either expressed or implied, of any organization.
+ * #L%
+ */
+
+package org.scijava.annotations;
+
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.lang.annotation.Annotation;
+import java.net.URL;
+import java.util.Enumeration;
+import java.util.HashSet;
+import java.util.Set;
+
+import org.scijava.util.Combiner;
+import org.scijava.util.FileUtils;
+
+/**
+ * Combines SezPoz annotations from all JAR files on the classpath.
+ * 
+ * @author Curtis Rueden
+ */
+public class AnnotationCombiner extends AbstractIndexWriter implements Combiner
+{
+
+	private static final String PREFIX = "META-INF/json/";
+	private static final String LEGACY_PREFIX = "META-INF/annotations/";
+
+	/** Reads in annotations from all available resources and combines them. */
+	@Override
+	public void combine(File outputDirectory) throws Exception {
+		if (outputDirectory == null) {
+			outputDirectory = new File("src/main/assembly/all");
+		}
+		final Set<String> annotationFiles = getAnnotationFiles();
+
+		final ClassLoader loader = Thread.currentThread().getContextClassLoader();
+
+		log("");
+		log("Writing annotations to " + outputDirectory.getAbsolutePath());
+
+		new File(outputDirectory, PREFIX).mkdirs();
+		for (final String annotationFile : annotationFiles) {
+			final String annotationName = annotationFile.substring(PREFIX.length());
+			@SuppressWarnings("unchecked")
+			final Class<? extends Annotation> annotation =
+				(Class<? extends Annotation>) loader.loadClass(annotationName);
+			for (IndexItem<? extends Annotation> item : Index
+				.load(annotation, loader))
+			{
+				add(adapt(item.annotation()), annotationName, item.className());
+			}
+		}
+
+		write(new AnnotationStreamFactory(outputDirectory));
+	}
+
+	/** Scans for annotations files in every resource on the classpath. */
+	public Set<String> getAnnotationFiles() throws IOException {
+		final HashSet<String> files = new HashSet<String>();
+
+		for (final String prefix : new String[] { PREFIX, LEGACY_PREFIX }) {
+			final Enumeration<URL> directories =
+				Thread.currentThread().getContextClassLoader().getResources(prefix);
+			while (directories.hasMoreElements()) {
+				final URL url = directories.nextElement();
+				for (final URL annotationIndexURL : FileUtils.listContents(url)) {
+					String string = annotationIndexURL.toString();
+					if (string.endsWith("/")) {
+						continue;
+					}
+					final int length = string.length();
+					add(files, PREFIX +
+						string.substring(string.lastIndexOf('/', length - 1) + 1, length));
+				}
+			}
+		}
+		return files;
+	}
+
+	// -- Helper methods --
+
+	private void add(final HashSet<String> set, final String item) {
+		log("\t" + item);
+		set.add(item);
+	}
+
+	private void log(final String msg) {
+		System.out.println(msg);
+	}
+
+	// -- Helper Class --
+
+	/**
+	 * {@link StreamFactory} implementation for writing an annotation.
+	 *
+	 */
+	private static class AnnotationStreamFactory implements StreamFactory {
+
+		private final File outputDirectory;
+
+		public AnnotationStreamFactory(final File outputDirectory) {
+			this.outputDirectory = outputDirectory;
+		}
+
+		@Override
+		public InputStream openInput(String annotationName) throws IOException {
+			return null;
+		}
+
+		@Override
+		public OutputStream openOutput(String annotationName) throws IOException {
+			final File file = new File(outputDirectory, PREFIX + annotationName);
+			return new FileOutputStream(file);
+		}
+
+		@Override
+		public boolean isClassObsolete(String className) {
+			return false;
+		}
+
+	}
+
+	// -- Main method --
+
+	public static void main(final String[] args) throws Exception {
+		new AnnotationCombiner().combine(args.length > 0 ? new File(args[0]) : null);
+	}
+}
diff --git a/src/main/java/org/scijava/annotations/AnnotationProcessor.java b/src/main/java/org/scijava/annotations/AnnotationProcessor.java
@@ -1,8 +1,10 @@
 /*
  * #%L
- * Annotation index (processor and index access library).
+ * SciJava Common shared library for SciJava software.
  * %%
- * Copyright (C) 2009 - 2013 Board of Regents of the University of Wisconsin-Madison.
+ * Copyright (C) 2009 - 2013 Board of Regents of the University of
+ * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
+ * Institute of Molecular Cell Biology and Genetics.
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:

diff --git a/src/main/java/org/scijava/annotations/DirectoryIndexer.java b/src/main/java/org/scijava/annotations/DirectoryIndexer.java
@@ -1,8 +1,10 @@
 /*
  * #%L
- * Annotation index (processor and index access library).
+ * SciJava Common shared library for SciJava software.
  * %%
- * Copyright (C) 2009 - 2013 Board of Regents of the University of Wisconsin-Madison.
+ * Copyright (C) 2009 - 2013 Board of Regents of the University of
+ * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
+ * Institute of Molecular Cell Biology and Genetics.
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:

diff --git a/src/main/java/org/scijava/annotations/EclipseHelper.java b/src/main/java/org/scijava/annotations/EclipseHelper.java
@@ -1,8 +1,10 @@
 /*
  * #%L
- * Annotation index (processor and index access library).
+ * SciJava Common shared library for SciJava software.
  * %%
- * Copyright (C) 2009 - 2013 Board of Regents of the University of Wisconsin-Madison.
+ * Copyright (C) 2009 - 2013 Board of Regents of the University of
+ * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
+ * Institute of Molecular Cell Biology and Genetics.
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:

diff --git a/src/main/java/org/scijava/annotations/Index.java b/src/main/java/org/scijava/annotations/Index.java
@@ -1,8 +1,10 @@
 /*
  * #%L
- * Annotation index (processor and index access library).
+ * SciJava Common shared library for SciJava software.
  * %%
- * Copyright (C) 2009 - 2013 Board of Regents of the University of Wisconsin-Madison.
+ * Copyright (C) 2009 - 2013 Board of Regents of the University of
+ * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
+ * Institute of Molecular Cell Biology and Genetics.
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:

diff --git a/src/main/java/org/scijava/annotations/IndexItem.java b/src/main/java/org/scijava/annotations/IndexItem.java
@@ -1,8 +1,10 @@
 /*
  * #%L
- * Annotation index (processor and index access library).
+ * SciJava Common shared library for SciJava software.
  * %%
- * Copyright (C) 2009 - 2013 Board of Regents of the University of Wisconsin-Madison.
+ * Copyright (C) 2009 - 2013 Board of Regents of the University of
+ * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
+ * Institute of Molecular Cell Biology and Genetics.
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:

diff --git a/src/main/java/org/scijava/annotations/IndexReader.java b/src/main/java/org/scijava/annotations/IndexReader.java
@@ -1,8 +1,10 @@
 /*
  * #%L
- * Annotation index (processor and index access library).
+ * SciJava Common shared library for SciJava software.
  * %%
- * Copyright (C) 2009 - 2013 Board of Regents of the University of Wisconsin-Madison.
+ * Copyright (C) 2009 - 2013 Board of Regents of the University of
+ * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
+ * Institute of Molecular Cell Biology and Genetics.
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:

diff --git a/src/main/java/org/scijava/annotations/Indexable.java b/src/main/java/org/scijava/annotations/Indexable.java
@@ -1,8 +1,10 @@
 /*
  * #%L
- * Annotation index (processor and index access library).
+ * SciJava Common shared library for SciJava software.
  * %%
- * Copyright (C) 2009 - 2013 Board of Regents of the University of Wisconsin-Madison.
+ * Copyright (C) 2009 - 2013 Board of Regents of the University of
+ * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
+ * Institute of Molecular Cell Biology and Genetics.
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:

diff --git a/src/main/java/org/scijava/annotations/legacy/LegacyReader.java b/src/main/java/org/scijava/annotations/legacy/LegacyReader.java
@@ -1,8 +1,10 @@
 /*
  * #%L
- * Annotation index (processor and index access library).
+ * SciJava Common shared library for SciJava software.
  * %%
- * Copyright (C) 2009 - 2013 Board of Regents of the University of Wisconsin-Madison.
+ * Copyright (C) 2009 - 2013 Board of Regents of the University of
+ * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
+ * Institute of Molecular Cell Biology and Genetics.
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:

diff --git a/src/main/java/org/scijava/plugin/AbstractHandlerService.java b/src/main/java/org/scijava/plugin/AbstractHandlerService.java
@@ -1,6 +1,6 @@
 /*
  * #%L
- * ImageJ software for multidimensional image processing and analysis.
+ * SciJava Common shared library for SciJava software.
  * %%
  * Copyright (C) 2009 - 2013 Board of Regents of the University of
  * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck

diff --git a/src/main/java/org/scijava/plugin/AbstractPTService.java b/src/main/java/org/scijava/plugin/AbstractPTService.java
@@ -1,6 +1,6 @@
 /*
  * #%L
- * ImageJ software for multidimensional image processing and analysis.
+ * SciJava Common shared library for SciJava software.
  * %%
  * Copyright (C) 2009 - 2013 Board of Regents of the University of
  * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck

diff --git a/src/main/java/org/scijava/plugin/AbstractSingletonService.java b/src/main/java/org/scijava/plugin/AbstractSingletonService.java
@@ -1,6 +1,6 @@
 /*
  * #%L
- * ImageJ software for multidimensional image processing and analysis.
+ * SciJava Common shared library for SciJava software.
  * %%
  * Copyright (C) 2009 - 2013 Board of Regents of the University of
  * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck

diff --git a/src/main/java/org/scijava/plugin/AbstractTypedPlugin.java b/src/main/java/org/scijava/plugin/AbstractTypedPlugin.java
@@ -1,6 +1,6 @@
 /*
  * #%L
- * ImageJ software for multidimensional image processing and analysis.
+ * SciJava Common shared library for SciJava software.
  * %%
  * Copyright (C) 2009 - 2013 Board of Regents of the University of
  * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck

diff --git a/src/main/java/org/scijava/plugin/AbstractTypedService.java b/src/main/java/org/scijava/plugin/AbstractTypedService.java
@@ -1,6 +1,6 @@
 /*
  * #%L
- * ImageJ software for multidimensional image processing and analysis.
+ * SciJava Common shared library for SciJava software.
  * %%
  * Copyright (C) 2009 - 2013 Board of Regents of the University of
  * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck

diff --git a/src/main/java/org/scijava/plugin/AbstractWrapperPlugin.java b/src/main/java/org/scijava/plugin/AbstractWrapperPlugin.java
@@ -1,6 +1,6 @@
 /*
  * #%L
- * ImageJ software for multidimensional image processing and analysis.
+ * SciJava Common shared library for SciJava software.
  * %%
  * Copyright (C) 2009 - 2013 Board of Regents of the University of
  * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck

diff --git a/src/main/java/org/scijava/plugin/AbstractWrapperService.java b/src/main/java/org/scijava/plugin/AbstractWrapperService.java
@@ -1,6 +1,6 @@
 /*
  * #%L
- * ImageJ software for multidimensional image processing and analysis.
+ * SciJava Common shared library for SciJava software.
  * %%
  * Copyright (C) 2009 - 2013 Board of Regents of the University of
  * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck