Payara blue merge prior to release 163

appserver/admingui/payara-console-extras/src/main/resources/notification/notification.jsf

@@ -58,7 +58,7 @@
                     mapPut(map="#{pageSession.valueMap}" key="dynamic" value="#{pageSession.dynamic}");
                     mapPut(map="#{pageSession.valueMap}" key="notifierDynamic" value="#{pageSession.notifierDynamic}");
                     prepareSuccessfulMsg();
-                    gf.updateEntity(endpoint="#{sessionScope.REST_URL}/set-notification" attrs="#{pageSession.valueMap}" convertToFalse="#{pageSession.convertToFalseList}");
+                    gf.updateEntity(endpoint="#{sessionScope.REST_URL}/set-notification-configuration" attrs="#{pageSession.valueMap}" convertToFalse="#{pageSession.convertToFalseList}");
                     />
             </sun:button>
         </sun:panelGroup>

appserver/admingui/payara-console-extras/src/main/resources/requestTracing/requestTracing.jsf

@@ -58,7 +58,7 @@
                     mapPut(map="#{pageSession.valueMap}" key="dynamic" value="#{pageSession.dynamic}");
                     mapPut(map="#{pageSession.valueMap}" key="notifierDynamic" value="#{pageSession.notifierDynamic}");
                     prepareSuccessfulMsg();
-                    gf.updateEntity(endpoint="#{sessionScope.REST_URL}/set-requesttracing" attrs="#{pageSession.valueMap}" convertToFalse="#{pageSession.convertToFalseList}");
+                    gf.updateEntity(endpoint="#{sessionScope.REST_URL}/set-requesttracing-configuration" attrs="#{pageSession.valueMap}" convertToFalse="#{pageSession.convertToFalseList}");
                     />
             </sun:button>
         </sun:panelGroup>

appserver/payara-appserver-modules/jmx-monitoring-service/src/main/java/fish/payara/jmx/monitoring/admin/EnableMonitoringServiceOnDas.java

@@ -0,0 +1,76 @@
+/*
+ DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
+ Copyright (c) 2016 C2B2 Consulting Limited. All rights reserved.
+ The contents of this file are subject to the terms of the Common Development
+ and Distribution License("CDDL") (collectively, the "License").  You
+ may not use this file except in compliance with the License.  You can
+ obtain a copy of the License at
+ https://glassfish.dev.java.net/public/CDDL+GPL_1_1.html
+ or packager/legal/LICENSE.txt.  See the License for the specific
+ language governing permissions and limitations under the License.
+ When distributing the software, include this License Header Notice in each
+ file and include the License file at packager/legal/LICENSE.txt.
+ */
+package fish.payara.jmx.monitoring.admin;
+
+import com.sun.enterprise.config.serverbeans.Domain;
+import fish.payara.jmx.monitoring.MonitoringService;
+import java.util.Properties;
+import javax.inject.Inject;
+import org.glassfish.api.ActionReport;
+import org.glassfish.api.I18n;
+import org.glassfish.api.Param;
+import org.glassfish.api.admin.AdminCommand;
+import org.glassfish.api.admin.AdminCommandContext;
+import org.glassfish.api.admin.CommandLock;
+import org.glassfish.api.admin.ExecuteOn;
+import org.glassfish.api.admin.RestEndpoint;
+import org.glassfish.api.admin.RestEndpoints;
+import org.glassfish.api.admin.RuntimeType;
+import org.glassfish.config.support.CommandTarget;
+import org.glassfish.config.support.TargetType;
+import org.glassfish.hk2.api.PerLookup;
+import org.jvnet.hk2.annotations.Service;
+
+/**
+ *
+ * @author savage
+ */
+@Service(name = "__enable-monitoring-service-on-das")
+@PerLookup
+@CommandLock(CommandLock.LockType.NONE)
+@I18n("__enable-monitoring-service-on-das")
+@ExecuteOn(RuntimeType.DAS)
+@TargetType(value = {CommandTarget.DAS, CommandTarget.STANDALONE_INSTANCE, CommandTarget.CLUSTER, CommandTarget.CLUSTERED_INSTANCE, CommandTarget.CONFIG})
+@RestEndpoints({
+    @RestEndpoint(configBean = Domain.class,
+            opType = RestEndpoint.OpType.GET,
+            path = "__enable-monitoring-service-on-das",
+            description = "Enables the JMX Monitoring Service on the DAS")
+})
+public class EnableMonitoringServiceOnDas implements AdminCommand {
+
+    @Inject 
+    MonitoringService monitoringService;
+
+    @Param(name = "enabled", optional = false)
+    private Boolean enabled;
+
+    @Param(name = "target", optional = true, defaultValue = "server")
+    protected String target;
+
+    @Override
+    public void execute(AdminCommandContext context) {
+
+        final ActionReport actionReport = context.getActionReport();
+        Properties extraProperties = actionReport.getExtraProperties();
+        if (extraProperties == null) {
+            extraProperties = new Properties();
+            actionReport.setExtraProperties(extraProperties);
+        }
+
+        monitoringService.setEnabled(enabled);
+        actionReport.appendMessage("The JMX Monitoring Service status set to " + enabled + " on " + target);
+    }
+
+}

appserver/payara-appserver-modules/jmx-monitoring-service/src/main/java/fish/payara/jmx/monitoring/admin/EnableMonitoringServiceOnInstance.java

@@ -0,0 +1,77 @@
+/*
+ DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
+ Copyright (c) 2016 C2B2 Consulting Limited. All rights reserved.
+ The contents of this file are subject to the terms of the Common Development
+ and Distribution License("CDDL") (collectively, the "License").  You
+ may not use this file except in compliance with the License.  You can
+ obtain a copy of the License at
+ https://glassfish.dev.java.net/public/CDDL+GPL_1_1.html
+ or packager/legal/LICENSE.txt.  See the License for the specific
+ language governing permissions and limitations under the License.
+ When distributing the software, include this License Header Notice in each
+ file and include the License file at packager/legal/LICENSE.txt.
+ */
+package fish.payara.jmx.monitoring.admin;
+
+import com.sun.enterprise.config.serverbeans.Domain;
+import fish.payara.jmx.monitoring.MonitoringService;
+import java.util.Properties;
+import javax.inject.Inject;
+import org.glassfish.api.ActionReport;
+import org.glassfish.api.I18n;
+import org.glassfish.api.Param;
+import org.glassfish.api.admin.AdminCommand;
+import org.glassfish.api.admin.AdminCommandContext;
+import org.glassfish.api.admin.CommandLock;
+import org.glassfish.api.admin.ExecuteOn;
+import org.glassfish.api.admin.RestEndpoint;
+import org.glassfish.api.admin.RestEndpoints;
+import org.glassfish.api.admin.RuntimeType;
+import org.glassfish.config.support.CommandTarget;
+import org.glassfish.config.support.TargetType;
+import org.glassfish.hk2.api.PerLookup;
+import org.jboss.logging.Logger;
+import org.jvnet.hk2.annotations.Service;
+
+/**
+ *
+ * @author savage
+ */
+@Service(name = "__enable-monitoring-service-on-instance")
+@PerLookup
+@CommandLock(CommandLock.LockType.NONE)
+@I18n("__enable-monitoring-service-on-instance")
+@ExecuteOn(RuntimeType.INSTANCE)
+@TargetType(value = {CommandTarget.DAS, CommandTarget.STANDALONE_INSTANCE, CommandTarget.CLUSTER, CommandTarget.CLUSTERED_INSTANCE, CommandTarget.CONFIG})
+@RestEndpoints({
+    @RestEndpoint(configBean = Domain.class,
+            opType = RestEndpoint.OpType.GET,
+            path = "__enable-monitoring-service-on-instance",
+            description = "Enables the JMX Monitoring Service on Instance")
+})
+public class EnableMonitoringServiceOnInstance implements AdminCommand {
+
+    @Inject 
+    MonitoringService monitoringService;
+
+    @Param(name = "enabled", optional = false)
+    private Boolean enabled;
+
+    @Param(name = "target", optional = true, defaultValue = "server")
+    protected String target;
+
+    @Override
+    public void execute(AdminCommandContext context) {
+
+        final ActionReport actionReport = context.getActionReport();
+        Properties extraProperties = actionReport.getExtraProperties();
+        if (extraProperties == null) {
+            extraProperties = new Properties();
+            actionReport.setExtraProperties(extraProperties);
+        }
+
+        monitoringService.setEnabled(enabled);
+        actionReport.appendMessage("The JMX Monitoring Service status set to " + enabled + " on " + target);
+    }
+
+}

appserver/payara-appserver-modules/jmx-monitoring-service/src/main/java/fish/payara/jmx/monitoring/admin/GetMonitoringConfiguration.java

@@ -17,6 +17,7 @@ and Distribution License("CDDL") (collectively, the "License").  You
 import com.sun.enterprise.config.serverbeans.Domain;
 import com.sun.enterprise.util.ColumnFormatter;
 import com.sun.enterprise.util.StringUtils;
+import com.sun.enterprise.util.SystemPropertyConstants;
 import fish.payara.jmx.monitoring.configuration.MonitoringServiceConfiguration;
 import javax.inject.Inject;
 import org.glassfish.api.ActionReport;
@@ -46,7 +47,7 @@ and Distribution License("CDDL") (collectively, the "License").  You
 @CommandLock(CommandLock.LockType.NONE)
 @I18n("get.monitoring.configuration")
 @ExecuteOn(value = {RuntimeType.DAS})
-@TargetType(value = {CommandTarget.DAS, CommandTarget.STANDALONE_INSTANCE, CommandTarget.CLUSTER})
+@TargetType(value = {CommandTarget.DAS, CommandTarget.STANDALONE_INSTANCE, CommandTarget.CLUSTER, CommandTarget.CLUSTERED_INSTANCE, CommandTarget.CONFIG})
 @RestEndpoints({
     @RestEndpoint(configBean = Domain.class,
             opType = RestEndpoint.OpType.GET,
@@ -63,7 +64,7 @@ public class GetMonitoringConfiguration implements AdminCommand {
     @Param(name = "pretty", defaultValue = "false", optional = true)
     private Boolean pretty;
 
-    @Param(name = "target", defaultValue = "server", optional = true)
+    @Param(name = "target", defaultValue = SystemPropertyConstants.DAS_SERVER_NAME, optional = true)
     private String target;
 
     /**

appserver/payara-appserver-modules/jmx-monitoring-service/src/main/java/fish/payara/jmx/monitoring/admin/SetMonitoringConfiguration.java

@@ -28,7 +28,9 @@ and Distribution License("CDDL") (collectively, the "License").  You
 import org.glassfish.api.admin.AdminCommand;
 import org.glassfish.api.admin.AdminCommandContext;
 import org.glassfish.api.admin.CommandLock;
+import org.glassfish.api.admin.CommandRunner;
 import org.glassfish.api.admin.ExecuteOn;
+import org.glassfish.api.admin.ParameterMap;
 import org.glassfish.api.admin.RestEndpoint;
 import org.glassfish.api.admin.RestEndpoints;
 import org.glassfish.api.admin.RuntimeType;
@@ -52,8 +54,8 @@ and Distribution License("CDDL") (collectively, the "License").  You
 @PerLookup
 @CommandLock(CommandLock.LockType.NONE)
 @I18n("set.monitoring.configuration")
-@ExecuteOn(RuntimeType.INSTANCE)
-@TargetType(value = {CommandTarget.DAS, CommandTarget.STANDALONE_INSTANCE, CommandTarget.CLUSTER})
+@ExecuteOn(RuntimeType.DAS)
+@TargetType(value = {CommandTarget.DAS, CommandTarget.STANDALONE_INSTANCE, CommandTarget.CLUSTER, CommandTarget.CLUSTERED_INSTANCE, CommandTarget.CONFIG})
 @RestEndpoints({
     @RestEndpoint(configBean = Domain.class,
             opType = RestEndpoint.OpType.GET,
@@ -63,7 +65,7 @@ and Distribution License("CDDL") (collectively, the "License").  You
 public class SetMonitoringConfiguration implements AdminCommand {
 
     @Inject
-    ServiceLocator habitat;
+    ServiceLocator serviceLocator;
 
     @Inject
     protected Target targetUtil;
@@ -100,7 +102,7 @@ public void execute(AdminCommandContext context) {
         final ActionReport actionReport = context.getActionReport();
         Config config = targetUtil.getConfig(target);
 
-        final MonitoringService service = habitat.getService(MonitoringService.class);
+        final MonitoringService service = serviceLocator.getService(MonitoringService.class);
         if (service == null) {
             actionReport.appendMessage("Could not find a monitoring service.");
             actionReport.setActionExitCode(ActionReport.ExitCode.FAILURE);
@@ -118,9 +120,9 @@ public Object run(final MonitoringServiceConfiguration monitoringConfigProxy) th
                     return monitoringConfigProxy;
                 }
             }, monitoringConfig);
-                    
+
             if (dynamic) {
-                monitoringService.setEnabled(enabled);
+                enableOnTarget(actionReport, context, enabled);
             }
 
         } catch (TransactionFailure ex) {
@@ -153,6 +155,25 @@ private void updateConfiguration(MonitoringServiceConfiguration monitoringConfig
         }
     }
 
+    private void enableOnTarget(ActionReport actionReport, AdminCommandContext context, Boolean enabled) {
+        CommandRunner runner = serviceLocator.getService(CommandRunner.class);
+        ActionReport subReport = context.getActionReport().addSubActionsReport();
+        CommandRunner.CommandInvocation invocation;
+
+        if (target.equals("server-config")) {
+            invocation = runner.getCommandInvocation("__enable-monitoring-service-on-das", subReport, context.getSubject());
+        } else {
+            invocation = runner.getCommandInvocation("__enable-monitoring-service-on-instance", subReport, context.getSubject());
+        }
+
+        // Build the parameters
+        ParameterMap params = new ParameterMap();
+        params.add("enabled", enabled.toString());
+        params.add("target", target);
+        invocation.parameters(params);
+        invocation.execute();
+    }
+
     /**
      * Updates monitoring attributes through adding a new property and/or deleting an existing one.
      *

appserver/web/web-core/src/main/java/org/apache/catalina/fileupload/PartItem.java

@@ -56,7 +56,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-
+// Portions Copyright [2016] [C2B2 Consulting Limited and/or its affiliates]
 package org.apache.catalina.fileupload;
 
 import org.apache.catalina.Globals;
@@ -739,6 +739,24 @@ private void readObject(ObjectInputStream in)
             throws IOException, ClassNotFoundException {
         // read values
         in.defaultReadObject();
+
+        // PAYARA-953 protect against null byte attacks 
+        if (repository != null) {
+            if (repository.getPath().contains("\0")) {
+                throw new IOException("Repository path cannot contain a null byte");
+            }
+
+            if (!repository.isDirectory()) {
+                throw new IOException("Repository path " + repository.getPath() + " is not a directory ");
+            }
+        }
+
+        if (dfosFile != null) {
+            if (dfosFile.getPath().contains("\0")) {
+                throw new IOException("File path cannot contain a null byte");
+            }
+        }
+        // END PAYARA-953
 
         OutputStream output = getOutputStream();
         if (cachedContent != null) {

nucleus/payara-modules/healthcheck-core/src/main/java/fish/payara/nucleus/healthcheck/HealthCheckService.java

@@ -132,4 +132,12 @@ public void shutdownHealthCheck() {
             Logger.getLogger(HealthCheckService.class.getName()).log(Level.INFO, "Payara Health Check Service is shutdown.");
         }
     }
+
+    public BaseHealthCheck getCheck(String serviceName) {
+        return registeredTasks.get(serviceName).getCheck();
+    }
+
+    public HealthCheckServiceConfiguration getConfiguration() {
+        return configuration;
+    }
 }