Clean up warnings

Finally updating the Mongo API cleared a number of warnings; this commit
clears up the rest.

src/us/kbase/typedobj/test/BasicValidationTest.java

@@ -127,12 +127,12 @@ public static Collection<Object[]> assembleTestInstanceList() throws Exception {
 		prepareDb();
 		Object [][] instanceInfo = new Object[validInstanceResources.size()+invalidInstanceResources.size()][2];
 		for(int k=0; k<validInstanceResources.size(); k++) {
-			instanceInfo[k][0] = new Integer(k);
-			instanceInfo[k][1] = new Boolean(true);
+			instanceInfo[k][0] = k;
+			instanceInfo[k][1] = true;
 		}
 		for(int k=0; k<invalidInstanceResources.size(); k++) {
-			instanceInfo[k+validInstanceResources.size()][0] = new Integer(k);
-			instanceInfo[k+validInstanceResources.size()][1] = new Boolean(false);
+			instanceInfo[k+validInstanceResources.size()][0] = k;
+			instanceInfo[k+validInstanceResources.size()][1] = false;
 		}
 
 		return Arrays.asList(instanceInfo);

src/us/kbase/typedobj/test/DetailedValidationTest.java

@@ -113,7 +113,7 @@ public static Collection<Object[]> assembleTestInstanceList() throws Exception {
 		prepareDb();
 		Object [][] instanceInfo = new Object[resources.size()][1];
 		for(int k=0; k<resources.size(); k++) {
-			instanceInfo[k][0] = new Integer(k);
+			instanceInfo[k][0] = k;
 		}
 
 		return Arrays.asList(instanceInfo);

src/us/kbase/typedobj/test/ObjectExtractionByPathTest.java

@@ -100,7 +100,7 @@ public static Collection<Object[]> assembleTestInstanceList() throws Exception {
 		if(VERBOSE) System.out.println(" " + instanceResources.size() + " found");
 		Object [][] instanceInfo = new Object[instanceResources.size()][1];
 		for(int k=0; k<instanceResources.size(); k++) {
-			instanceInfo[k][0] = new Integer(k);
+			instanceInfo[k][0] = k;
 		}
 		return Arrays.asList(instanceInfo);
 	}

src/us/kbase/workspace/kbase/InitWorkspaceServer.java

@@ -2,6 +2,7 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.lang.reflect.InvocationTargetException;
 import java.net.MalformedURLException;
 import java.net.URISyntaxException;
 import java.net.URL;
@@ -395,8 +396,9 @@ private static WorkspaceEventListenerFactory loadFac(final String className)
 		final Class<WorkspaceEventListenerFactory> inter =
 				(Class<WorkspaceEventListenerFactory>) cls;
 		try {
-			return inter.newInstance();
-		} catch (IllegalAccessException | InstantiationException e) {
+			return inter.getDeclaredConstructor().newInstance();
+		} catch (IllegalAccessException | InstantiationException | IllegalArgumentException |
+				InvocationTargetException | NoSuchMethodException | SecurityException e) {
 			throw new WorkspaceInitException(String.format(
 					"Module %s could not be instantiated: %s", className, e.getMessage()), e);
 		}

src/us/kbase/workspace/test/controllers/shock/ShockController.java

@@ -24,14 +24,13 @@
 import org.apache.commons.io.IOUtils;
 import org.apache.velocity.VelocityContext;
 import org.apache.velocity.app.Velocity;
+import org.bson.Document;
 
-import com.mongodb.BasicDBObject;
-import com.mongodb.DB;
-import com.mongodb.DBObject;
 import com.mongodb.MongoClient;
 import com.mongodb.MongoClientOptions;
 import com.mongodb.MongoCredential;
 import com.mongodb.ServerAddress;
+import com.mongodb.client.MongoDatabase;
 
 /** Q&D Utility to run a Shock server for the purposes of testing from
  * Java.
@@ -101,7 +100,7 @@ public ShockController(
 		generateConfig(SHOCK_CONFIG, context, shockcfg);
 
 		final MongoClient mc = buildMongo(mongohost, shockMongoDBname, mongouser, mongopwd);
-		final DB shockDB = mc.getDB(shockMongoDBname);
+		final MongoDatabase shockDB = mc.getDatabase(shockMongoDBname);
 
 		setupWorkarounds(shockDB, adminUser, knownVersion);
 
@@ -129,8 +128,10 @@ private MongoClient buildMongo(
 		}
 	}
 
-	private void setupWorkarounds(DB shockDB, String adminUser,
-			String version) {
+	private void setupWorkarounds(
+			final MongoDatabase shockDB,
+			final String adminUser,
+			final String version) {
 		if ("0.8.23".equals(version)) {
 			// the version of 0.8.23 above actually works fine without this,
 			// but it's a few commits beyond the actual 0.8.23 tag, so if the
@@ -147,25 +148,28 @@ private void setupWorkarounds(DB shockDB, String adminUser,
 		}
 	}
 
-	private void addAdminUser(DB shockDB, String adminUser) {
-		final DBObject a = new BasicDBObject("username", adminUser);
+	private void addAdminUser(final MongoDatabase shockDB, final String adminUser) {
+		final Document a = new Document("username", adminUser);
 		a.put("uuid", "095abbb0-07cc-43b3-8fd9-98edfb2541be");
 		a.put("fullname", "");
 		a.put("email", "");
 		a.put("password", "");
 		a.put("shock_admin", true);
-		shockDB.getCollection("Users").save(a);
+		shockDB.getCollection("Users").insertOne(a);
 	}
 
-	private void setCollectionVersions(DB shockDB, int nodever,
-			int aclver, int authver) {
-		final DBObject n = new BasicDBObject("name", "Node");
+	private void setCollectionVersions(
+			final MongoDatabase shockDB,
+			int nodever,
+			int aclver,
+			int authver) {
+		final Document n = new Document("name", "Node");
 		n.put("version", nodever);
-		final DBObject acl = new BasicDBObject("name", "ACL");
+		final Document acl = new Document("name", "ACL");
 		acl.put("version", aclver);
-		final DBObject auth = new BasicDBObject("name", "Auth");
+		final Document auth = new Document("name", "Auth");
 		auth.put("version", authver);
-		shockDB.getCollection("Versions").insert(Arrays.asList(n, acl, auth));
+		shockDB.getCollection("Versions").insertMany(Arrays.asList(n, acl, auth));
 	}
 
 	/** Returns the Shock version supplied in the constructor *if* the version

test/debugging/jsonclientcaller/JsonClientCaller.java

@@ -275,7 +275,7 @@ public <ARG, RET> RET jsonrpcCall(String method, ARG arg,
 			if (retError != null) {
 				String data = retError.get("data") == null ? retError.get("error") : retError.get("data");
 				throw new ServerException(retError.get("message"),
-						new Integer(retError.get("code")), retError.get("name"),
+						Integer.valueOf(retError.get("code")), retError.get("name"),
 						data);
 			}
 			if (res == null && ret)

test/performance/ConfigurationsAndThreads.java

@@ -150,7 +150,6 @@ public static void timeReadWrite(int writes, String user, String pwd, String sho
 //		us.kbase.workspace.test.WorkspaceTestCommonDeprecated.destroyAndSetupDB(
 //				1, WorkspaceTestCommon.SHOCK, user, null);
 		//NOTE this setup is just to make it compile, not tested yet
-		@SuppressWarnings("resource")
 		final MongoClient mc = new MongoClient(MONGO_HOST);
 		MC = mc;
 		final TypeDefinitionDB typeDefDB = new TypeDefinitionDB(
@@ -238,16 +237,16 @@ private static Perf measurePerformance(int writes, int threads,
 		for (int i = 0; i < threads; i++) {
 			if (i + 1 == threads) {
 				int threadSize = writes - pos;
-				rwthreads[i] = clazz.newInstance();
+				rwthreads[i] = clazz.getDeclaredConstructor().newInstance();
 				rwthreads[i].initialize(threadSize, i + 1);
 				threadDist.add(threadSize);
 			} else if (hasMod && i % 2 == 1) {
-				rwthreads[i] = clazz.newInstance();
+				rwthreads[i] = clazz.getDeclaredConstructor().newInstance();
 				rwthreads[i].initialize(minWrites + 1, i + 1);
 				pos += minWrites + 1;
 				threadDist.add(minWrites + 1);
 			} else {
-				rwthreads[i] = clazz.newInstance();
+				rwthreads[i] = clazz.getDeclaredConstructor().newInstance();
 				rwthreads[i].initialize(minWrites, i + 1);
 				pos += minWrites;
 				threadDist.add(minWrites);

test/performance/PerformanceMeasurement.java

@@ -72,7 +72,7 @@ public static double stddev(final double mean, final List<Long> values,
 		final double pop = population ? 0 : -1;
 		double accum = 0;
 		for (Long d: values) {
-			accum += Math.pow(new Double(d) - mean, 2);
+			accum += Math.pow(Double.valueOf(d) - mean, 2);
 		}
 		return Math.sqrt(accum / (values.size() + pop));
 	}

war/web.xml

@@ -1,8 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <web-app>
-    <listener>
-        <listener-class>us.kbase.workspace.kbase.AppEventListener</listener-class>
-    </listener>
     <servlet>
         <servlet-name>RootServlet</servlet-name>
         <servlet-class>us.kbase.workspace.WorkspaceServer</servlet-class>