add file-based caching for annotations - was taking waaaaay too long to

look them up from the hosting MN each time they were read. cache will be
cleared when the app container (typically tomcat) is restarted.

src/main/java/org/dataone/annotator/store/FileBasedCache.java

@@ -0,0 +1,52 @@
+package org.dataone.annotator.store;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.HashMap;
+import java.util.Map;
+
+import org.apache.commons.io.IOUtils;
+
+public class FileBasedCache {
+
+	private static Map<String, File> cache = new HashMap<String, File>();	
+
+	public static void cache(String id, InputStream is) throws IOException {
+		if (!cache.containsKey(id)) {
+			File file = File.createTempFile("annotator_cache", ".dat");
+			file.deleteOnExit();
+			IOUtils.copy(is, new FileOutputStream(file));
+			cache.put(id, file);
+		}
+	}
+
+	public static InputStream get(String id) throws FileNotFoundException {
+
+		if (cache.containsKey(id)) {
+			File file = cache.get(id);
+			return new FileInputStream(file);
+		}
+
+		return null;
+	}
+
+	public static boolean remove(String id) {
+		if (cache.containsKey(id)) {
+			File file = cache.get(id);
+			file.delete();
+			return true;
+		}
+		return false;
+	}
+
+	public static void clear() {
+		for (File file: cache.values()) {
+			file.delete();
+		}
+		cache.clear();
+	}
+}

src/main/java/org/dataone/annotator/store/JsonAnnotatorStore.java

@@ -204,7 +204,13 @@ public String read(String id) throws Exception {
 		// read the annotation out as a String object
 		Identifier sid = new Identifier();
 		sid.setValue(id);
-		InputStream object = storageNode.get(session, sid);
+		InputStream object = FileBasedCache.get(id);
+		if (object == null) {
+			object = storageNode.get(session, sid);
+			FileBasedCache.cache(id, object);
+			object = FileBasedCache.get(id);
+		}
+
 		return IOUtils.toString(object, "UTF-8");
 	}
 
@@ -255,6 +261,7 @@ public String update(String id, String partialAnnotationContent) throws Exceptio
 		// update it on the node
 		InputStream object = new ByteArrayInputStream(annotation.toJSONString().getBytes(DEFAULT_ENCODING));
 		storageNode.update(session, originalPid, object, pid, sysmeta);
+		FileBasedCache.remove(id);
 
 		return annotation.toJSONString();
 
@@ -270,6 +277,9 @@ public void delete(String id) throws Exception {
 		sid.setValue(id);
 
 		storageNode.archive(session, sid);
+
+		FileBasedCache.remove(id);
+
 		//TODO: allow deletes by anyone, not just the node admin
 		//storageNode.delete(session, sid);