add cache for docId to Doc mapping

A Doc does not change once it is created, so it is easy to cache.
Speedup was from 1ms per Doc to 3ms for 444 Docs (0.00675ms/Doc).

data-store/src/main/java/org/lucares/pdb/datastore/internal/DataStore.java

@@ -2,6 +2,7 @@ package org.lucares.pdb.datastore.internal;
 
 import java.io.IOException;
 import java.nio.file.Path;
+import java.time.Duration;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
@@ -29,6 +30,7 @@ import org.lucares.pdb.map.PersistentMap;
 import org.lucares.pdb.map.PersistentMap.EncoderDecoder;
 import org.lucares.utils.Preconditions;
 import org.lucares.utils.byteencoder.VariableByteEncoder;
+import org.lucares.utils.cache.HotEntryCache;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -148,6 +150,10 @@ public class DataStore implements AutoCloseable {
 
 	private final PersistentMap<Tag, Long> tagToDocsId;
 
+	// A Doc will never be changed once it is created. Therefore we can cache them
+	// easily.
+	private final HotEntryCache<Long, Doc> docIdToDocCache = new HotEntryCache<>(Duration.ofMinutes(10));
+
 	private final DiskStorage diskStorage;
 	private final Path diskStorageFilePath;
 	private final Path storageBasePath;
@@ -287,32 +293,48 @@ public class DataStore implements AutoCloseable {
 
 		synchronized (docIdToDoc) {
 
+			final long start = System.nanoTime();
 			for (int i = 0; i < docIdsList.size(); i++) {
 				final long docId = docIdsList.get(i);
 
-				final Doc doc = docIdToDoc.getValue(docId);
+				final Doc doc = getDocByDocId(docId);
 				Objects.requireNonNull(doc, "Doc with id " + docId + " did not exist.");
 
 				result.add(doc);
 			}
+			System.out.println(
+					"mapDocIdsToDocs: " + (System.nanoTime() - start) / 1_000_000.0 + "ms ; tags:" + result.size());
 		}
 		return result;
 	}
 
 	public List<Doc> getByTags(final Tags tags) {
+		final long start = System.nanoTime();
 		try {
 			final Long docId = tagsToDocId.getValue(tags);
 			final List<Doc> result = new ArrayList<>(0);
 			if (docId != null) {
-				final Doc doc = docIdToDoc.getValue(docId);
+				final Doc doc = getDocByDocId(docId);
 				result.add(doc);
 			}
+			System.out
+					.println("getByTags: " + (System.nanoTime() - start) / 1_000_000.0 + "ms ; tags:" + result.size());
 			return result;
 		} catch (final IOException e) {
 			throw new RuntimeIOException(e);
 		}
 	}
 
+	private Doc getDocByDocId(final Long docId) {
+		return docIdToDocCache.putIfAbsent(docId, k -> {
+			try {
+				return docIdToDoc.getValue(k);
+			} catch (final IOException e) {
+				throw new RuntimeIOException(e);
+			}
+		});
+	}
+
 	@Override
 	public void close() throws IOException {
 		try {

pdb-utils/build.gradle

@@ -1,4 +1,4 @@
 
 dependencies {
-	
+	compile lib_guava
 }

pdb-utils/src/main/java/org/lucares/utils/cache/HotEntryCache.java

@@ -1,4 +1,4 @@
-package org.lucares.performance.db;
+package org.lucares.utils.cache;
 
 import java.time.Clock;
 import java.time.Duration;
@@ -12,20 +12,22 @@ import java.util.concurrent.ScheduledExecutorService;
 import java.util.concurrent.TimeUnit;
 import java.util.concurrent.atomic.AtomicReference;
 import java.util.function.Consumer;
-
+import java.util.function.Function;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 
 import com.google.common.util.concurrent.ThreadFactoryBuilder;
 
 /**
  * A cache that only keeps 'hot' entries, that is entries that have been
  * accessed recently. Entries that have not been accessed recently are removed.
+ * <p>
+ * Caching frameworks like EhCache only evict entries when a new entry is added.
+ * That might not be desired, e.g. when the cached objects block resources.
+ * <p>
+ * This cache is a simple wrapper for a ConcurrentHashMap that evicts entries
+ * after timeToLive+5s.
  */
 public class HotEntryCache<K, V> {
 
-	private static final Logger LOGGER = LoggerFactory.getLogger(HotEntryCache.class);
-
 	public enum EventType {
 		EVICTED, REMOVED
 	}
@@ -150,6 +152,32 @@ public class HotEntryCache<K, V> {
 		return oldValue.get() != null ? oldValue.get().getValue() : null;
 	}
 
+	/**
+	 * Puts the value supplied by the mappingFunction, if the key does not already
+	 * exist in the map. The operation is done atomically, that is the function is
+	 * executed at most once. This method is blocking while other threads are
+	 * computing the mapping function. Therefore the computation should be short and
+	 * simple.
+	 *
+	 * @param key             key of the value
+	 * @param mappingFunction a function that returns the value that should be
+	 *                        inserted
+	 * @return the newly inserted or existing value, or null if
+	 *         {@code mappingFunction} returned {@code null}
+	 */
+	public V putIfAbsent(final K key, final Function<K, V> mappingFunction) {
+
+		final Entry<V> entry = cache.computeIfAbsent(key, (k) -> {
+			final V value = mappingFunction.apply(k);
+			return new Entry<>(value, clock);
+		});
+
+		if (entry != null) {
+			entry.touch(clock);
+		}
+		return entry != null ? entry.getValue() : null;
+	}
+
 	public V remove(final K key) {
 
 		final AtomicReference<Entry<V>> oldValue = new AtomicReference<>();
@@ -175,7 +203,6 @@ public class HotEntryCache<K, V> {
 	}
 
 	private void evict() {
-		LOGGER.trace("running evict");
 		for (final K key : cache.keySet()) {
 
 			cache.computeIfPresent(key, (k, e) -> {

pdb-utils/src/test/java/org/lucares/utils/cache/HotEntryCacheTest.java

@@ -1,15 +1,18 @@
-package org.lucares.performance.db;
+package org.lucares.utils.cache;
 
 import java.time.Duration;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 import java.util.concurrent.CompletableFuture;
+import java.util.concurrent.CountDownLatch;
 import java.util.concurrent.ExecutionException;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
 import java.util.concurrent.TimeUnit;
 import java.util.concurrent.TimeoutException;
 
-import org.lucares.performance.db.HotEntryCache.EventType;
+import org.lucares.utils.cache.HotEntryCache.EventType;
 import org.testng.Assert;
 import org.testng.annotations.Test;
 
@@ -126,4 +129,92 @@ public class HotEntryCacheTest {
 
 		Assert.assertEquals(cache.get("key"), null);
 	}
+
+	/**
+	 * Checks that
+	 * {@link HotEntryCache#putIfAbsent(Object, java.util.function.Function)
+	 * putIfAbsent} is atomic by calling
+	 * {@link HotEntryCache#putIfAbsent(Object, java.util.function.Function)
+	 * putIfAbsent} in two threads and asserting that the supplier was only called
+	 * once.
+	 *
+	 * @throws Exception
+	 */
+	public void testPutIfAbsentIsAtomic() throws Exception {
+		final HotEntryCache<String, String> cache = new HotEntryCache<>(Duration.ofSeconds(10));
+
+		final ExecutorService pool = Executors.newCachedThreadPool();
+		try {
+			final CountDownLatch latch = new CountDownLatch(1);
+
+			final String key = "key";
+			final String valueA = "A";
+			final String valueB = "B";
+
+			pool.submit(() -> {
+				cache.putIfAbsent(key, k -> {
+					latch.countDown();
+					sleep(TimeUnit.MILLISECONDS, 20);
+					return valueA;
+				});
+				return null;
+			});
+			pool.submit(() -> {
+				waitFor(latch);
+				cache.putIfAbsent(key, k -> valueB);
+				return null;
+			});
+
+			pool.shutdown();
+			pool.awaitTermination(1, TimeUnit.MINUTES);
+
+			final String actual = cache.get(key);
+			Assert.assertEquals(actual, valueA);
+		} finally {
+			pool.shutdownNow();
+		}
+	}
+
+	public void testPutIfAbsentReturnsExistingValue() throws Exception {
+		final HotEntryCache<String, String> cache = new HotEntryCache<>(Duration.ofSeconds(10));
+
+		final String key = "key";
+		final String valueA = "A";
+		final String valueB = "B";
+
+		cache.put(key, valueA);
+
+		final String returnedByPutIfAbsent = cache.putIfAbsent(key, k -> valueB);
+		Assert.assertEquals(returnedByPutIfAbsent, valueA);
+
+		final String actualInCache = cache.get(key);
+		Assert.assertEquals(actualInCache, valueA);
+	}
+
+	public void testPutIfAbsentDoesNotAddNull() throws Exception {
+		final HotEntryCache<String, String> cache = new HotEntryCache<>(Duration.ofSeconds(10));
+
+		final String key = "key";
+		final String returnedByPutIfAbsent = cache.putIfAbsent(key, k -> null);
+		Assert.assertNull(returnedByPutIfAbsent, null);
+
+		final String actualInCache = cache.get(key);
+		Assert.assertEquals(actualInCache, null);
+	}
+
+	private void sleep(final TimeUnit timeUnit, final long timeout) {
+		try {
+			timeUnit.sleep(timeout);
+		} catch (final InterruptedException e) {
+			throw new IllegalStateException(e);
+		}
+	}
+
+	private void waitFor(final CountDownLatch latch) {
+		try {
+			latch.await(1, TimeUnit.MINUTES);
+		} catch (final InterruptedException e) {
+			throw new IllegalStateException(e);
+		}
+	}
 }

pdb-utils/src/test/java/org/lucares/utils/cache/ModifiableFixedTimeClock.java

@@ -1,4 +1,4 @@
-package org.lucares.performance.db;
+package org.lucares.utils.cache;
 
 import java.io.Serializable;
 import java.time.Clock;
@@ -60,7 +60,7 @@ public class ModifiableFixedTimeClock extends Clock implements Serializable {
 
 	@Override
 	public Clock withZone(final ZoneId zone) {
-		if (zone.equals(this.zone)) { // intentional NPE
+		if (zone.equals(this.zone)) {
 			return this;
 		}
 		return new ModifiableFixedTimeClock(instant, zone);

performanceDb/src/main/java/org/lucares/performance/db/TagsToFile.java

@@ -9,9 +9,10 @@ import java.util.function.Consumer;
 import org.lucares.pdb.api.Tags;
 import org.lucares.pdb.datastore.Doc;
 import org.lucares.pdb.datastore.internal.DataStore;
-import org.lucares.performance.db.HotEntryCache.Event;
+import org.lucares.utils.cache.HotEntryCache;
-import org.lucares.performance.db.HotEntryCache.EventListener;
+import org.lucares.utils.cache.HotEntryCache.Event;
-import org.lucares.performance.db.HotEntryCache.EventType;
+import org.lucares.utils.cache.HotEntryCache.EventListener;
+import org.lucares.utils.cache.HotEntryCache.EventType;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;