Cleanup bootstrap package.

* makes most classes final and package private
* removes duplicate and confusing multiple entry points
* adds javadocs to some classes like JarHell,Security
* adds a public class BootStrapInfo that exposes any stats
  needed by outside code.

core/src/main/java/org/elasticsearch/bootstrap/Bootstrap.java

@@ -21,15 +21,12 @@ package org.elasticsearch.bootstrap;
 
 import org.apache.lucene.util.Constants;
 import org.apache.lucene.util.StringHelper;
-import org.elasticsearch.ExceptionsHelper;
 import org.elasticsearch.Version;
 import org.elasticsearch.common.PidFile;
 import org.elasticsearch.common.SuppressForbidden;
 import org.elasticsearch.common.cli.CliTool;
 import org.elasticsearch.common.cli.Terminal;
 import org.elasticsearch.common.collect.Tuple;
-import org.elasticsearch.common.inject.CreationException;
-import org.elasticsearch.common.inject.spi.Message;
 import org.elasticsearch.common.lease.Releasables;
 import org.elasticsearch.common.logging.ESLogger;
 import org.elasticsearch.common.logging.Loggers;
@@ -44,16 +41,14 @@ import org.elasticsearch.node.NodeBuilder;
 import org.elasticsearch.node.internal.InternalSettingsPreparer;
 
 import java.util.Locale;
-import java.util.Set;
 import java.util.concurrent.CountDownLatch;
 
-import static com.google.common.collect.Sets.newHashSet;
 import static org.elasticsearch.common.settings.Settings.Builder.EMPTY_SETTINGS;
 
 /**
- * A main entry point when starting from the command line.
+ * Internal startup code.
  */
-public class Bootstrap {
+final class Bootstrap {
 
     private static volatile Bootstrap INSTANCE;
 
@@ -137,10 +132,6 @@ public class Bootstrap {
         OsProbe.getInstance();
     }
 
-    public static boolean isMemoryLocked() {
-        return Natives.isMemoryLocked();
-    }
-
     private void setup(boolean addShutdownHook, Settings settings, Environment environment) throws Exception {
         initializeNatives(settings.getAsBoolean("bootstrap.mlockall", false),
                 settings.getAsBoolean("bootstrap.ctrlhandler", true));
@@ -222,16 +213,11 @@ public class Bootstrap {
         }
     }
 
-    /** Calls doMain(), but with special formatting of errors */
+    /**
-    public static void main(String[] args) throws StartupError {
+     * This method is invoked by {@link Elasticsearch#main(String[])}
-        try {
+     * to startup elasticsearch.
-            doMain(args);
+     */
-        } catch (Throwable t) {
+    static void init(String[] args) throws Throwable {
-            throw new StartupError(t);
-        }
-    }
-
-    public static void doMain(String[] args) throws Throwable {
         BootstrapCLIParser bootstrapCLIParser = new BootstrapCLIParser();
         CliTool.ExitStatus status = bootstrapCLIParser.execute(args);
 

core/src/main/java/org/elasticsearch/bootstrap/BootstrapCLIParser.java

@@ -38,7 +38,7 @@ import java.util.Properties;
 import static org.elasticsearch.common.cli.CliToolConfig.Builder.cmd;
 import static org.elasticsearch.common.cli.CliToolConfig.Builder.optionBuilder;
 
-public class BootstrapCLIParser extends CliTool {
+final class BootstrapCLIParser extends CliTool {
 
     private static final CliToolConfig CONFIG = CliToolConfig.config("elasticsearch", BootstrapCLIParser.class)
             .cmds(Start.CMD, Version.CMD)

core/src/main/java/org/elasticsearch/bootstrap/BootstrapInfo.java

@@ -0,0 +1,46 @@
+/*
+ * Licensed to Elasticsearch under one or more contributor
+ * license agreements. See the NOTICE file distributed with
+ * this work for additional information regarding copyright
+ * ownership. Elasticsearch licenses this file to you under
+ * the Apache License, Version 2.0 (the "License"); you may
+ * not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+
+package org.elasticsearch.bootstrap;
+
+/** 
+ * Exposes system startup information 
+ */
+public final class BootstrapInfo {
+
+    /** no instantiation */
+    private BootstrapInfo() {}
+    
+    /** 
+     * Returns true if we successfully loaded native libraries.
+     * <p>
+     * If this returns false, then native operations such as locking
+     * memory did not work.
+     */
+    public static boolean isNativesAvailable() {
+        return Natives.JNA_AVAILABLE;
+    }
+    
+    /** 
+     * Returns true if we were able to lock the process's address space.
+     */
+    public static boolean isMemoryLocked() {
+        return Natives.isMemoryLocked();
+    }
+}

core/src/main/java/org/elasticsearch/bootstrap/Elasticsearch.java

@@ -20,11 +20,23 @@
 package org.elasticsearch.bootstrap;
 
 /**
- * A wrapper around {@link Bootstrap} just so the process will look nicely on things like jps.
+ * This class starts elasticsearch.
  */
-public class Elasticsearch extends Bootstrap {
+public final class Elasticsearch {
 
+    /** no instantiation */
+    private Elasticsearch() {}
+
+    /**
+     * Main entry point for starting elasticsearch
+     */
     public static void main(String[] args) throws StartupError {
-        Bootstrap.main(args);
+        try {
+            Bootstrap.init(args);
+        } catch (Throwable t) {
+            // format exceptions to the console in a special way
+            // to avoid 2MB stacktraces from guice, etc.
+            throw new StartupError(t);
+        }
     }
 }

core/src/main/java/org/elasticsearch/bootstrap/JNACLibrary.java

@@ -59,7 +59,7 @@ final class JNACLibrary {
         public long rlim_max = 0;
         
         @Override
-        protected List getFieldOrder() {
+        protected List<String> getFieldOrder() {
             return Arrays.asList(new String[] { "rlim_cur", "rlim_max" });
         }
     }

core/src/main/java/org/elasticsearch/bootstrap/JNAKernel32Library.java

@@ -35,7 +35,7 @@ import java.util.List;
 /**
  * Library for Windows/Kernel32
  */
-class JNAKernel32Library {
+final class JNAKernel32Library {
 
     private static final ESLogger logger = Loggers.getLogger(JNAKernel32Library.class);
 
@@ -148,7 +148,7 @@ class JNAKernel32Library {
         public NativeLong Type;
 
         @Override
-        protected List getFieldOrder() {
+        protected List<String> getFieldOrder() {
             return Arrays.asList(new String[]{"BaseAddress", "AllocationBase", "AllocationProtect", "RegionSize", "State", "Protect", "Type"});
         }
     }

core/src/main/java/org/elasticsearch/bootstrap/JNANatives.java

@@ -34,10 +34,13 @@ import static org.elasticsearch.bootstrap.JNAKernel32Library.SizeT;
  */
 class JNANatives {
 
+    /** no instantiation */
+    private JNANatives() {}
+
     private static final ESLogger logger = Loggers.getLogger(JNANatives.class);
 
     // Set to true, in case native mlockall call was successful
-    public static boolean LOCAL_MLOCKALL = false;
+    static boolean LOCAL_MLOCKALL = false;
 
     static void tryMlockall() {
         int errno = Integer.MIN_VALUE;

core/src/main/java/org/elasticsearch/bootstrap/JVMCheck.java

@@ -29,6 +29,8 @@ import java.util.Map;
 
 /** Checks that the JVM is ok and won't cause index corruption */
 final class JVMCheck {
+    /** no instantiation */
+    private JVMCheck() {}
     
     /**
      * URL with latest JVM recommendations

core/src/main/java/org/elasticsearch/bootstrap/JarHell.java

@@ -25,7 +25,6 @@ import org.elasticsearch.common.io.PathUtils;
 import org.elasticsearch.common.logging.ESLogger;
 import org.elasticsearch.common.logging.Loggers;
 
-import java.io.ByteArrayInputStream;
 import java.io.IOException;
 import java.net.URL;
 import java.net.URLClassLoader;
@@ -34,14 +33,34 @@ import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.SimpleFileVisitor;
 import java.nio.file.attribute.BasicFileAttributes;
-import java.util.*;
+import java.util.Arrays;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Locale;
+import java.util.Map;
+import java.util.Set;
 import java.util.jar.JarEntry;
 import java.util.jar.JarFile;
 import java.util.jar.Manifest;
 
-/** Simple check for duplicate class files across the classpath */
+/**
+ * Simple check for duplicate class files across the classpath.
+ * <p>
+ * This class checks for incompatibilities in the following ways:
+ * <ul>
+ *   <li>Checks that class files are not duplicated across jars.</li>
+ *   <li>Checks any {@code X-Compile-Target-JDK} value in the jar
+ *       manifest is compatible with current JRE</li>
+ *   <li>Checks any {@code X-Compile-Elasticsearch-Version} value in
+ *       the jar manifest is compatible with the current ES</li>
+ * </ul>
+ */
 public class JarHell {
 
+    /** no instantiation */
+    private JarHell() {}
+
     /** Simple driver class, can be used eg. from builds. Returns non-zero on jar-hell */
     @SuppressForbidden(reason = "command line tool")
     public static void main(String args[]) throws Exception {

core/src/main/java/org/elasticsearch/bootstrap/Natives.java

@@ -26,27 +26,32 @@ import org.elasticsearch.common.logging.Loggers;
  * The Natives class is a wrapper class that checks if the classes necessary for calling native methods are available on
  * startup. If they are not available, this class will avoid calling code that loads these classes.
  */
-class Natives {
+final class Natives {
+    /** no instantiation */
+    private Natives() {}
+
     private static final ESLogger logger = Loggers.getLogger(Natives.class);
 
     // marker to determine if the JNA class files are available to the JVM
-    private static boolean jnaAvailable = false;
+    static final boolean JNA_AVAILABLE;
 
     static {
+        boolean v = false;
         try {
             // load one of the main JNA classes to see if the classes are available. this does not ensure that all native
             // libraries are available, only the ones necessary by JNA to function
             Class.forName("com.sun.jna.Native");
-            jnaAvailable = true;
+            v = true;
         } catch (ClassNotFoundException e) {
             logger.warn("JNA not found. native methods will be disabled.", e);
         } catch (UnsatisfiedLinkError e) {
             logger.warn("unable to load JNA native support library, native methods will be disabled.", e);
         }
+        JNA_AVAILABLE = v;
     }
 
     static void tryMlockall() {
-        if (!jnaAvailable) {
+        if (!JNA_AVAILABLE) {
             logger.warn("cannot mlockall because JNA is not available");
             return;
         }
@@ -54,7 +59,7 @@ class Natives {
     }
 
     static boolean definitelyRunningAsRoot() {
-        if (!jnaAvailable) {
+        if (!JNA_AVAILABLE) {
             logger.warn("cannot check if running as root because JNA is not available");
             return false;
         }
@@ -62,7 +67,7 @@ class Natives {
     }
 
     static void tryVirtualLock() {
-        if (!jnaAvailable) {
+        if (!JNA_AVAILABLE) {
             logger.warn("cannot mlockall because JNA is not available");
             return;
         }
@@ -70,7 +75,7 @@ class Natives {
     }
 
     static void addConsoleCtrlHandler(ConsoleCtrlHandler handler) {
-        if (!jnaAvailable) {
+        if (!JNA_AVAILABLE) {
             logger.warn("cannot register console handler because JNA is not available");
             return;
         }
@@ -78,7 +83,7 @@ class Natives {
     }
 
     static boolean isMemoryLocked() {
-        if (!jnaAvailable) {
+        if (!JNA_AVAILABLE) {
             return false;
         }
         return JNANatives.LOCAL_MLOCKALL;

core/src/main/java/org/elasticsearch/bootstrap/Security.java

@@ -38,15 +38,59 @@ import java.util.Map;
 import java.util.regex.Pattern;
 
 /** 
- * Initializes securitymanager with necessary permissions.
+ * Initializes SecurityManager with necessary permissions.
  * <p>
- * We use a template file (the one we test with), and add additional 
+ * <h1>Initialization</h1>
- * permissions based on the environment (data paths, etc)
+ * The JVM is not initially started with security manager enabled,
+ * instead we turn it on early in the startup process. This is a tradeoff
+ * between security and ease of use:
+ * <ul>
+ *   <li>Assigns file permissions to user-configurable paths that can
+ *       be specified from the command-line or {@code elasticsearch.yml}.</li>
+ *   <li>Allows for some contained usage of native code that would not
+ *       otherwise be permitted.</li>
+ * </ul>
+ * <p>
+ * <h1>Permissions</h1>
+ * Permissions use a policy file packaged as a resource, this file is
+ * also used in tests. File permissions are generated dynamically and
+ * combined with this policy file.
+ * <p>
+ * For each configured path, we ensure it exists and is accessible before
+ * granting permissions, otherwise directory creation would require
+ * permissions to parent directories.
+ * <p>
+ * In some exceptional cases, permissions are assigned to specific jars only,
+ * when they are so dangerous that general code should not be granted the
+ * permission, but there are extenuating circumstances.
+ * <p>
+ * Groovy scripts are assigned no permissions. This does not provide adequate
+ * sandboxing, as these scripts still have access to ES classes, and could
+ * modify members, etc that would cause bad things to happen later on their
+ * behalf (no package protections are yet in place, this would need some
+ * cleanups to the scripting apis). But still it can provide some defense for users
+ * that enable dynamic scripting without being fully aware of the consequences.
+ * <p>
+ * <h1>Disabling Security</h1>
+ * SecurityManager can be disabled completely with this setting:
+ * <pre>
+ * es.security.manager.enabled = false
+ * </pre>
+ * <p>
+ * <h1>Debugging Security</h1>
+ * A good place to start when there is a problem is to turn on security debugging:
+ * <pre>
+ * JAVA_OPTS="-Djava.security.debug=access:failure" bin/elasticsearch
+ * </pre>
+ * See <a href="https://docs.oracle.com/javase/7/docs/technotes/guides/security/troubleshooting-security.html">
+ * Troubleshooting Security</a> for information.
  */
 final class Security {
+    /** no instantiation */
+    private Security() {}
        
     /** 
-     * Initializes securitymanager for the environment
+     * Initializes SecurityManager for the environment
      * Can only happen once!
      */
     static void configure(Environment environment) throws Exception {

core/src/main/java/org/elasticsearch/bootstrap/StartupError.java

@@ -32,7 +32,7 @@ import java.io.PrintStream;
  */
 //TODO: remove this when guice is removed, and exceptions are cleaned up
 //this is horrible, but its what we must do
-class StartupError extends RuntimeException {
+final class StartupError extends RuntimeException {
     
     /** maximum length of a stacktrace, before we truncate it */
     static final int STACKTRACE_LIMIT = 30;

core/src/main/java/org/elasticsearch/common/inject/spi/Elements.java

@@ -19,7 +19,6 @@ package org.elasticsearch.common.inject.spi;
 import com.google.common.collect.ImmutableList;
 import com.google.common.collect.Lists;
 import com.google.common.collect.Sets;
-import org.elasticsearch.bootstrap.Bootstrap;
 import org.elasticsearch.common.inject.*;
 import org.elasticsearch.common.inject.binder.AnnotatedBindingBuilder;
 import org.elasticsearch.common.inject.binder.AnnotatedConstantBindingBuilder;
@@ -343,7 +342,7 @@ public final class Elements {
             return builder;
         }
 
-        private static ESLogger logger = Loggers.getLogger(Bootstrap.class);
+        private static ESLogger logger = Loggers.getLogger(Elements.class);
 
         protected Object getSource() {
             Object ret;

core/src/main/java/org/elasticsearch/monitor/process/ProcessProbe.java

@@ -19,7 +19,7 @@
 
 package org.elasticsearch.monitor.process;
 
-import org.elasticsearch.bootstrap.Bootstrap;
+import org.elasticsearch.bootstrap.BootstrapInfo;
 
 import java.lang.management.ManagementFactory;
 import java.lang.management.OperatingSystemMXBean;
@@ -136,7 +136,7 @@ public class ProcessProbe {
     }
 
     public ProcessInfo processInfo() {
-        return new ProcessInfo(jvmInfo().pid(), Bootstrap.isMemoryLocked());
+        return new ProcessInfo(jvmInfo().pid(), BootstrapInfo.isMemoryLocked());
     }
 
     public ProcessStats processStats() {

core/src/test/java/org/elasticsearch/benchmark/mapping/ManyMappingsBenchmark.java

@@ -21,7 +21,7 @@ package org.elasticsearch.benchmark.mapping;
 
 import org.elasticsearch.action.bulk.BulkRequestBuilder;
 import org.elasticsearch.action.support.IndicesOptions;
-import org.elasticsearch.bootstrap.Bootstrap;
+import org.elasticsearch.bootstrap.BootstrapForTesting;
 import org.elasticsearch.client.Client;
 import org.elasticsearch.common.settings.Settings;
 import org.elasticsearch.common.unit.TimeValue;
@@ -85,7 +85,7 @@ public class ManyMappingsBenchmark {
 
     public static void main(String[] args) throws Exception {
         System.setProperty("es.logger.prefix", "");
-        Bootstrap.initializeNatives(true, false);
+        BootstrapForTesting.ensureInitialized();
         Settings settings = settingsBuilder()
                 .put("")
                 .put(SETTING_NUMBER_OF_SHARDS, 5)

core/src/test/java/org/elasticsearch/benchmark/recovery/ReplicaRecoveryBenchmark.java

@@ -20,7 +20,7 @@ package org.elasticsearch.benchmark.recovery;
 
 import org.elasticsearch.action.admin.indices.recovery.RecoveryResponse;
 import org.elasticsearch.action.admin.indices.recovery.ShardRecoveryResponse;
-import org.elasticsearch.bootstrap.Bootstrap;
+import org.elasticsearch.bootstrap.BootstrapForTesting;
 import org.elasticsearch.client.Client;
 import org.elasticsearch.cluster.metadata.IndexMetaData;
 import org.elasticsearch.cluster.routing.allocation.decider.DiskThresholdDecider;
@@ -57,7 +57,7 @@ public class ReplicaRecoveryBenchmark {
 
     public static void main(String[] args) throws Exception {
         System.setProperty("es.logger.prefix", "");
-        Bootstrap.initializeNatives(true, false);
+        BootstrapForTesting.ensureInitialized();
 
         Settings settings = settingsBuilder()
                 .put("gateway.type", "local")

core/src/test/java/org/elasticsearch/benchmark/search/aggregations/GlobalOrdinalsBenchmark.java

@@ -21,12 +21,13 @@ package org.elasticsearch.benchmark.search.aggregations;
 import com.carrotsearch.hppc.IntIntHashMap;
 import com.carrotsearch.hppc.ObjectHashSet;
 import com.carrotsearch.randomizedtesting.generators.RandomStrings;
+
 import org.elasticsearch.action.admin.cluster.health.ClusterHealthResponse;
 import org.elasticsearch.action.admin.cluster.stats.ClusterStatsResponse;
 import org.elasticsearch.action.bulk.BulkRequestBuilder;
 import org.elasticsearch.action.search.SearchResponse;
 import org.elasticsearch.benchmark.search.aggregations.TermsAggregationSearchBenchmark.StatsResult;
-import org.elasticsearch.bootstrap.Bootstrap;
+import org.elasticsearch.bootstrap.BootstrapForTesting;
 import org.elasticsearch.client.Client;
 import org.elasticsearch.common.settings.Settings;
 import org.elasticsearch.common.unit.ByteSizeValue;
@@ -66,7 +67,7 @@ public class GlobalOrdinalsBenchmark {
 
     public static void main(String[] args) throws Exception {
         System.setProperty("es.logger.prefix", "");
-        Bootstrap.initializeNatives(true, false);
+        BootstrapForTesting.ensureInitialized();
         Random random = new Random();
 
         Settings settings = settingsBuilder()

core/src/test/java/org/elasticsearch/benchmark/search/aggregations/SubAggregationSearchCollectModeBenchmark.java

@@ -27,7 +27,7 @@ import org.elasticsearch.action.admin.cluster.stats.ClusterStatsResponse;
 import org.elasticsearch.action.bulk.BulkRequestBuilder;
 import org.elasticsearch.action.bulk.BulkResponse;
 import org.elasticsearch.action.search.SearchResponse;
-import org.elasticsearch.bootstrap.Bootstrap;
+import org.elasticsearch.bootstrap.BootstrapForTesting;
 import org.elasticsearch.client.Client;
 import org.elasticsearch.client.Requests;
 import org.elasticsearch.common.StopWatch;
@@ -71,7 +71,7 @@ public class SubAggregationSearchCollectModeBenchmark {
     static Node[] nodes;
 
     public static void main(String[] args) throws Exception {
-        Bootstrap.initializeNatives(true, false);
+        BootstrapForTesting.ensureInitialized();
         Random random = new Random();
 
         Settings settings = settingsBuilder()

core/src/test/java/org/elasticsearch/benchmark/search/aggregations/TermsAggregationSearchAndIndexingBenchmark.java

@@ -20,13 +20,14 @@ package org.elasticsearch.benchmark.search.aggregations;
 
 import com.carrotsearch.hppc.ObjectScatterSet;
 import com.carrotsearch.randomizedtesting.generators.RandomStrings;
+
 import org.elasticsearch.action.admin.cluster.health.ClusterHealthResponse;
 import org.elasticsearch.action.admin.cluster.stats.ClusterStatsResponse;
 import org.elasticsearch.action.bulk.BulkRequestBuilder;
 import org.elasticsearch.action.bulk.BulkResponse;
 import org.elasticsearch.action.get.GetResponse;
 import org.elasticsearch.action.search.SearchResponse;
-import org.elasticsearch.bootstrap.Bootstrap;
+import org.elasticsearch.bootstrap.BootstrapForTesting;
 import org.elasticsearch.client.Client;
 import org.elasticsearch.client.Requests;
 import org.elasticsearch.common.settings.Settings;
@@ -71,7 +72,7 @@ public class TermsAggregationSearchAndIndexingBenchmark {
     static Node[] nodes;
 
     public static void main(String[] args) throws Exception {
-        Bootstrap.initializeNatives(true, false);
+        BootstrapForTesting.ensureInitialized();
         Settings settings = settingsBuilder()
                 .put("refresh_interval", "-1")
                 .put(SETTING_NUMBER_OF_SHARDS, 1)

core/src/test/java/org/elasticsearch/benchmark/search/aggregations/TermsAggregationSearchBenchmark.java

@@ -28,7 +28,7 @@ import org.elasticsearch.action.bulk.BulkRequestBuilder;
 import org.elasticsearch.action.bulk.BulkResponse;
 import org.elasticsearch.action.search.SearchRequestBuilder;
 import org.elasticsearch.action.search.SearchResponse;
-import org.elasticsearch.bootstrap.Bootstrap;
+import org.elasticsearch.bootstrap.BootstrapForTesting;
 import org.elasticsearch.client.Client;
 import org.elasticsearch.client.Requests;
 import org.elasticsearch.common.StopWatch;
@@ -99,7 +99,7 @@ public class TermsAggregationSearchBenchmark {
     }
 
     public static void main(String[] args) throws Exception {
-        Bootstrap.initializeNatives(true, false);
+        BootstrapForTesting.ensureInitialized();
         Random random = new Random();
 
         Settings settings = settingsBuilder()

core/src/test/java/org/elasticsearch/monitor/process/ProcessProbeTests.java

@@ -20,7 +20,7 @@
 package org.elasticsearch.monitor.process;
 
 import org.apache.lucene.util.Constants;
-import org.elasticsearch.bootstrap.Bootstrap;
+import org.elasticsearch.bootstrap.BootstrapInfo;
 import org.elasticsearch.test.ESTestCase;
 import org.junit.Test;
 
@@ -37,7 +37,7 @@ public class ProcessProbeTests extends ESTestCase {
         assertNotNull(info);
         assertThat(info.getRefreshInterval(), greaterThanOrEqualTo(0L));
         assertThat(info.getId(), equalTo(jvmInfo().pid()));
-        assertThat(info.isMlockall(), equalTo(Bootstrap.isMemoryLocked()));
+        assertThat(info.isMlockall(), equalTo(BootstrapInfo.isMemoryLocked()));
     }
 
     @Test