lib: use StampedLock, and fix check in GenericRestWSServer, #TASK-6565

On branch TASK-6565
Changes to be committed:
	modified:   cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/DataReleaseSingleton.java
	modified:   cellbase-server/src/main/java/org/opencb/cellbase/server/rest/GenericRestWSServer.java

cellbase-lib/src/main/java/org/opencb/cellbase/lib/impl/core/DataReleaseSingleton.java

@@ -29,7 +29,7 @@
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
-import java.util.concurrent.locks.ReentrantReadWriteLock;
+import java.util.concurrent.locks.StampedLock;
 
 public final class DataReleaseSingleton {
 
@@ -38,7 +38,7 @@ public final class DataReleaseSingleton {
     // {key = dbname, value = assembly}
     private Map<String, String> assemblyMap = new HashMap<>();
     // {key = dbname, value = lock}
-    private Map<String, ReentrantReadWriteLock> rwLockMap = new HashMap<>();
+    private Map<String, StampedLock> stampedLockMap = new HashMap<>();
 
     // {key = dbname, value = { key = release, value = { key = data, value = collection } } }
     private Map<String, Map<Integer, Map<String, MongoDBCollection>>> cachedData = new HashMap<>();
@@ -64,7 +64,7 @@ private DataReleaseSingleton(CellBaseManagerFactory managerFactory) {
                 // manager from the species and the assembly
                 speciesMap.put(databaseName, vertebrate.getId());
                 assemblyMap.put(databaseName, assembly.getName());
-                rwLockMap.put(databaseName, new ReentrantReadWriteLock());
+                stampedLockMap.put(databaseName, new StampedLock());
                 cachedData.put(databaseName, new HashMap<>());
             }
         }
@@ -89,6 +89,7 @@ public static DataReleaseSingleton getInstance() {
     private void loadData(String dbname) throws CellBaseException {
         String species = speciesMap.get(dbname);
         String assembly = assemblyMap.get(dbname);
+        // We need the release adaptor to get the collection name
         ReleaseMongoDBAdaptor releaseMongoDBAdaptor = managerFactory.getDataReleaseManager(species, assembly).getReleaseDBAdaptor();
         List<DataRelease> dataReleases = releaseMongoDBAdaptor.getAll().getResults();
         if (CollectionUtils.isNotEmpty(dataReleases)) {
@@ -118,16 +119,60 @@ public void checkDataRelease(String dbname, int release, String data) throws Cel
             String msg = UNKOWN_DATABASE_MSG_PREFIX + dbname;
             throw new CellBaseException(msg);
         }
-        rwLockMap.get(dbname).writeLock().lock();
+        long stamp = stampedLockMap.get(dbname).readLock();
         try {
-            if (!cachedData.containsKey(dbname) || !cachedData.containsKey(release)
-                    || (StringUtils.isNotEmpty(data) && !cachedData.get(release).containsKey(data))) {
-                loadData(dbname);
+            if (isCacheOutdated(dbname, release, data)) {
+                long writeStamp = stampedLockMap.get(dbname).tryConvertToWriteLock(stamp);
+                if (writeStamp != 0L) {
+                    // Successfully converted to write lock
+                    stamp = writeStamp;
+                    if (isCacheOutdated(dbname, release, data)) {
+                        loadData(dbname);
+                        checkAfterLoading(dbname, release, data);
+                    }
+                } else {
+                    // Could not convert to write lock, acquire it explicitly
+                    stampedLockMap.get(dbname).unlockRead(stamp);
+                    writeStamp = stampedLockMap.get(dbname).writeLock();
+                    try {
+                        if (isCacheOutdated(dbname, release, data)) {
+                            loadData(dbname);
+                            checkAfterLoading(dbname, release, data);
+                        }
+                    } finally {
+                        stampedLockMap.get(dbname).unlockWrite(writeStamp);
+                    }
+                }
             }
         } finally {
-            rwLockMap.get(dbname).writeLock().unlock();
+            stampedLockMap.get(dbname).unlockRead(stamp);
+        }
+    }
+
+    // Method to get collection name based on the data and the release
+    public MongoDBCollection getMongoDBCollection(String dbname, String data, int release) throws CellBaseException {
+        checkDataRelease(dbname, release, data);
+        return cachedData.get(dbname).get(release).get(data);
+    }
+
+    private boolean isCacheOutdated(String dbname, int release, String data) {
+        long stamp = stampedLockMap.get(dbname).tryOptimisticRead();
+        boolean outdated = !cachedData.get(dbname).containsKey(release)
+                || (StringUtils.isNotEmpty(data) && !cachedData.get(dbname).get(release).containsKey(data));
+        if (!stampedLockMap.get(dbname).validate(stamp)) {
+            // Fallback to read lock if optimistic read was invalidated
+            stamp = stampedLockMap.get(dbname).readLock();
+            try {
+                outdated = !cachedData.get(dbname).containsKey(release)
+                        || (StringUtils.isNotEmpty(data) && !cachedData.get(dbname).get(release).containsKey(data));
+            } finally {
+                stampedLockMap.get(dbname).unlockRead(stamp);
+            }
         }
+        return outdated;
+    }
 
+    private void checkAfterLoading(String dbname, int release, String data) throws CellBaseException {
         // Check after loading
         if (!cachedData.get(dbname).containsKey(release)) {
             // If the data release is invalid, throw an exception
@@ -141,10 +186,4 @@ public void checkDataRelease(String dbname, int release, String data) throws Cel
             throw new CellBaseException(msg);
         }
     }
-
-    // Method to get collection name based on the data and the release
-    public MongoDBCollection getMongoDBCollection(String dbname, String data, int release) throws CellBaseException {
-        checkDataRelease(dbname, release, data);
-        return cachedData.get(dbname).get(release).get(data);
-    }
 }

cellbase-server/src/main/java/org/opencb/cellbase/server/rest/GenericRestWSServer.java

@@ -225,9 +225,9 @@ protected int getDataRelease() throws CellBaseException {
                 if (dataRelease == 0) {
                     logger.info("Using data release 0 in query: using the default data release '" + defaultDataRelease.getRelease()
                             + "' for CellBase version '" + version + "'");
-                    DataReleaseSingleton.getInstance().checkDataRelease(species, assembly, version, dataRelease);
                     return defaultDataRelease.getRelease();
                 } else {
+                    DataReleaseSingleton.getInstance().checkDataRelease(species, assembly, version, dataRelease);
                     return dataRelease;
                 }
             } catch (NumberFormatException e) {