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RefApp Hibernate

PavolL
PavolL April 2, 2014 
Hi,

I have problem with RefApp and Hibernate-entitymanager.

When I add dependecy to hibernate-entitymanager and try to 

EntityManagerFactory emf = Persistence.createEntityManagerFactory("StudioDB", properties);

I have error: 

This XML file does not appear to have any style information associated with it. The document tree is shown below.
<status>
<status-code>500</status-code>
<message>org/w3c/dom/Node</message>
<stack-trace>
java.lang.NoClassDefFoundError: org/w3c/dom/Node
 at org.hibernate.ejb.Ejb3Configuration.configure(Ejb3Configuration.java:324)
 at org.hibernate.ejb.HibernatePersistence.createEntityManagerFactory(HibernatePersistence.java:56)
 at javax.persistence.Persistence.createEntityManagerFactory(Persistence.java:63)
 at com.honeywell.act.unity.um.rest.TestResource.testOrm(TestResource.java:75)
 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
 at java.lang.reflect.Method.invoke(Method.java:597)
 at com.atlassian.plugins.rest.common.interceptor.impl.DispatchProviderHelper$TypeOutInvoker$1.invoke(DispatchProviderHelper.java:205)
 at com.atlassian.plugins.rest.common.interceptor.impl.DispatchProviderHelper$1.intercept(DispatchProviderHelper.java:100)
 at com.atlassian.plugins.rest.common.interceptor.impl.DefaultMethodInvocation.invoke(DefaultMethodInvocation.java:61)
 at com.atlassian.plugins.rest.common.expand.interceptor.ExpandInterceptor.intercept(ExpandInterceptor.java:38)
 at com.atlassian.plugins.rest.common.interceptor.impl.DefaultMethodInvocation.invoke(DefaultMethodInvocation.java:61)
 at com.atlassian.plugins.rest.common.interceptor.impl.DispatchProviderHelper.invokeMethodWithInterceptors(DispatchProviderHelper.java:132)
 at com.atlassian.plugins.rest.common.interceptor.impl.DispatchProviderHelper$TypeOutInvoker._dispatch(DispatchProviderHelper.java:201)
 at com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(ResourceJavaMethodDispatcher.java:75)
 at com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.java:288)
 at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147)
 at com.sun.jersey.server.impl.uri.rules.ResourceClassRule.accept(ResourceClassRule.java:108)
 at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147)
 at com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootResourceClassesRule.java:84)
 at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1469)
 at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1400)
 at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1349)
 at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1339)
 at com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:416)
 at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:537)
 at com.atlassian.plugins.rest.module.RestDelegatingServletFilter$JerseyOsgiServletContainer.doFilter(RestDelegatingServletFilter.java:178)
 at com.sun.jersey.spi.container.servlet.ServletContainer.doFilter(ServletContainer.java:795)
 at com.atlassian.plugins.rest.module.RestDelegatingServletFilter.doFilter(RestDelegatingServletFilter.java:73)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:77)
 at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:63)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
 at com.atlassian.plugins.rest.module.servlet.RestServletUtilsUpdaterFilter.doFilterInternal(RestServletUtilsUpdaterFilter.java:26)
 at com.atlassian.plugins.rest.module.servlet.RestServletUtilsUpdaterFilter.doFilter(RestServletUtilsUpdaterFilter.java:40)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
 at com.atlassian.applinks.core.rest.context.ContextFilter.doFilter(ContextFilter.java:25)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
 at com.atlassian.prettyurls.filter.PrettyUrlsSiteMeshFixupFilter.doFilter(PrettyUrlsSiteMeshFixupFilter.java:36)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
 at com.atlassian.prettyurls.filter.PrettyUrlsDispatcherFilter.doFilter(PrettyUrlsDispatcherFilter.java:60)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
 at com.atlassian.prettyurls.filter.PrettyUrlsSiteMeshFilter.doFilter(PrettyUrlsSiteMeshFilter.java:92)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
 at com.atlassian.prettyurls.filter.PrettyUrlsMatcherFilter.doFilter(PrettyUrlsMatcherFilter.java:56)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
 at com.atlassian.labs.httpservice.resource.ResourceFilter.doFilter(ResourceFilter.java:59)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:77)
 at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:63)
 at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
 at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
 at com.opensymphony.sitemesh.webapp.SiteMeshFilter.obtainContent(SiteMeshFilter.java:129)
 at com.opensymphony.sitemesh.webapp.SiteMeshFilter.doFilter(SiteMeshFilter.java:77)
 at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
 at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:46)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
 at com.atlassian.prettyurls.filter.PrettyUrlsCombinedMatchDispatcherFilter.doFilter(PrettyUrlsCombinedMatchDispatcherFilter.java:61)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
 at com.atlassian.refapp.sal.ServletContextThreadLocalFilter.doFilter(ServletContextThreadLocalFilter.java:30)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:77)
 at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:63)
 at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
 at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:46)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
 at com.atlassian.refapp.auth.internal.AuthenticationContextCopyFilter.doFilter(AuthenticationContextCopyFilter.java:41)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
 at com.atlassian.seraph.filter.SecurityFilter.doFilter(SecurityFilter.java:219)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
 at com.atlassian.security.auth.trustedapps.filter.TrustedApplicationsFilter.doFilter(TrustedApplicationsFilter.java:100)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
 at com.atlassian.seraph.filter.BaseLoginFilter.doFilter(BaseLoginFilter.java:140)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
 at com.atlassian.oauth.serviceprovider.internal.servlet.OAuthFilter.doFilter(OAuthFilter.java:55)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
 at com.atlassian.plugins.rest.module.servlet.RestSeraphFilter.doFilter(RestSeraphFilter.java:44)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
 at com.atlassian.prettyurls.filter.PrettyUrlsCombinedMatchDispatcherFilter.doFilter(PrettyUrlsCombinedMatchDispatcherFilter.java:61)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:77)
 at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:63)
 at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
 at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:46)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
 at com.atlassian.refapp.decorator.PdlDarkToggleFilter.doFilter(PdlDarkToggleFilter.java:28)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
 at com.atlassian.fastdev.AutoReloadFilter.doFilter(AutoReloadFilter.java:63)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
 at com.atlassian.prettyurls.filter.PrettyUrlsCombinedMatchDispatcherFilter.doFilter(PrettyUrlsCombinedMatchDispatcherFilter.java:61)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:77)
 at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:63)
 at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
 at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
 at com.atlassian.plugin.refimpl.webresource.RequestCacheCleaner.doFilter(RequestCacheCleaner.java:28)
 at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
 at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
 at com.atlassian.plugin.refimpl.filter.RefAppFirstFilter.doFilter(RefAppFirstFilter.java:32)
 at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
 at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
 at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
 at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
 at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:128)
 at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
 at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:567)
 at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
 at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:293)
 at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:849)
 at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:583)
 at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:454)
 at java.lang.Thread.run(Thread.java:662)
 Caused by: java.lang.ClassNotFoundException: *** Class 'org.w3c.dom.Node' was not found because bundle com.honeywell.act.unity.portal.plugin.unity-usermgmt-plugin [68] does not import 'org.w3c.dom' even though bundle org.apache.felix.framework [0] does export it. Additionally, the class is also available from the system class loader. There are two fixes: 1) Add an import for 'org.w3c.dom' to bundle com.honeywell.act.unity.portal.plugin.unity-usermgmt-plugin [68]; imports are necessary for each class directly touched by bundle code or indirectly touched, such as super classes if their methods are used. 2) Add package 'org.w3c.dom' to the 'org.osgi.framework.bootdelegation' property; a library or VM bug can cause classes to be loaded by the wrong class loader. The first approach is preferable for preserving modularity. ***
 at org.apache.felix.framework.ModuleImpl$ModuleClassLoader.loadClass(ModuleImpl.java:1704)
 at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
 ... 153 more
 Caused by: java.lang.ClassNotFoundException: org.w3c.dom.Node
 at org.apache.felix.framework.ModuleImpl.findClassOrResourceByDelegation(ModuleImpl.java:772)
 at org.apache.felix.framework.ModuleImpl.access$200(ModuleImpl.java:73)
 at org.apache.felix.framework.ModuleImpl$ModuleClassLoader.loadClass(ModuleImpl.java:1690)
 ... 154 more
</stack-trace>
</status>

from code:

Rest service:

@GET
    @Produces
    @Path("orm")
    public String testOrm() {
        
            EntityManagerFactory emf = Persistence.createEntityManagerFactory("PU");
            EntityManager em = emf.createEntityManager();

My pom.xml is:

<?xml version="1.0" encoding="UTF-8"?>

<project xmlns="http://maven.apache.org/POM/4.0.0"
         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">

    <modelVersion>4.0.0</modelVersion>
    <groupId>com.honeywell.act.unity.portal.plugin</groupId>
    <artifactId>unity-usermgmt-plugin</artifactId>
    <version>1.0.0</version>

    <issueManagement>
        <system>JIRA</system>
        <url>https://acsjira.honeywell.com/browse/UNITY</url>
    </issueManagement>

    <scm>
        <connection>scm:svn:https://acssvn.honeywell.com/ACT/Tools/Unity/Modules/UserManagement/trunk</connection>
    </scm>

    <organization>
        <name>Honeywell International Sarl</name>
        <url>http://acstools.honeywell.com/</url>
    </organization>


    <name>Unity - User Management</name>
    <description>This is a ACT provided plugin extending the Unity Portal with User Management.</description>
    <packaging>atlassian-plugin</packaging>

    <dependencies>
        <dependency>
            <groupId>junit</groupId>
            <artifactId>junit</artifactId>
            <version>4.10</version>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>javax.servlet</groupId>
            <artifactId>servlet-api</artifactId>
            <version>2.4</version>
            <scope>provided</scope>
        </dependency>
        <dependency>
            <groupId>com.atlassian.sal</groupId>
            <artifactId>sal-api</artifactId>
            <version>2.7.1</version>
            <scope>provided</scope>
        </dependency>
        <dependency>
            <groupId>org.slf4j</groupId>
            <artifactId>slf4j-simple</artifactId>
            <version>1.5.8</version>
        </dependency>
        <!-- WIRED TEST RUNNER DEPENDENCIES -->
        <dependency>
            <groupId>com.atlassian.plugins</groupId>
            <artifactId>atlassian-plugins-osgi-testrunner</artifactId>
            <version>${plugin.testrunner.version}</version>
            <scope>test</scope>
        </dependency>

        <dependency>
            <groupId>javax.ws.rs</groupId>
            <artifactId>jsr311-api</artifactId>
            <version>1.1.1</version>
            <scope>provided</scope>
        </dependency>
        <dependency>
            <groupId>com.google.code.gson</groupId>
            <artifactId>gson</artifactId>
            <version>2.2.2-atlassian-1</version>
        </dependency>
        <dependency>
            <groupId>org.slf4j</groupId>
            <artifactId>slf4j-api</artifactId>
            <version>1.6.6</version>
            <scope>provided</scope>
        </dependency>
        <dependency>
            <groupId>org.mockito</groupId>
            <artifactId>mockito-all</artifactId>
            <version>1.8.5</version>
            <scope>test</scope>
        </dependency>
        <!-- HttpClient -->
        <dependency>
            <groupId>org.apache.httpcomponents</groupId>
            <artifactId>httpclient</artifactId>
            <version>4.3.2</version>
        </dependency>
        <!-- encoding authentication params -->
        <dependency>
            <groupId>com.sun.xml.security</groupId>
            <artifactId>xml-security-impl</artifactId>
            <version>1.0</version>
        </dependency>
        <!-- com.atlassian.plugins. -->
        <dependency>
            <groupId>com.atlassian.plugins</groupId>
            <artifactId>atlassian-plugins</artifactId>
            <version>2.0.0.rc2</version>
        </dependency>
        <!-- template renderer -->
        <dependency>
            <groupId>com.atlassian.templaterenderer</groupId>
            <artifactId>atlassian-template-renderer-api</artifactId>
            <version>1.3.1</version>
            <scope>provided</scope>
        </dependency>
        <!-- SOY templates -->
        <dependency>
            <groupId>com.atlassian.soy</groupId>
            <artifactId>soy-template-plugin</artifactId>
            <version>${soy.version}</version>
        </dependency>
        <dependency>
            <groupId>com.atlassian.soy</groupId>
            <artifactId>soy-template-renderer-api</artifactId>
            <version>${soy.version}</version>
        </dependency>
        <!-- Crowd client -->
        <dependency>
            <groupId>com.atlassian.crowd</groupId>
            <artifactId>crowd-integration-client</artifactId>
            <version>2.3.3</version>
        </dependency>
        <!-- SQL driver -->
        <dependency>
            <!-- Compatible with activeobjects-plugin -->
            <groupId>net.sourceforge.jtds</groupId>
            <artifactId>jtds</artifactId>
            <!-- 1.3.1 -->
            <version>1.2.4</version>
        </dependency>

        <dependency>
            <groupId>org.hibernate</groupId>
            <artifactId>hibernate-entitymanager</artifactId>
            <version>4.1.7.Final</version>
        </dependency>

        <!-- dependency-->
            <!-- groupId>dom4j</groupId-->
            <!-- artifactId>dom4j</artifactId-->
            <!-- version>1.6.1</version-->
        <!-- /dependency-->

        <!-- Unity Portal Bundled Plugins -->
        <dependency>
            <groupId>com.honeywell.softco.unity.portal</groupId>
            <artifactId>atlassian-refapp-auth-plugin</artifactId>
            <version>${unity.portal.version}</version>
            <scope>provided</scope>
        </dependency>
        <dependency>
            <groupId>com.honeywell.softco.unity.portal</groupId>
            <artifactId>unity-portal-decorator-plugin</artifactId>
            <version>${unity.portal.version}</version>
            <scope>provided</scope>
        </dependency>

    </dependencies>
    <dependencyManagement>
        <dependencies>
            <dependency>
                <groupId>com.atlassian.refapp</groupId>
                <artifactId>atlassian-platform</artifactId>
                <version>${refapp.version}</version>
                <type>pom</type>
                <scope>import</scope>
            </dependency>
        </dependencies>
    </dependencyManagement>
    <build>
        <plugins>
            <plugin>
                <groupId>com.atlassian.maven.plugins</groupId>
                <artifactId>maven-refapp-plugin</artifactId>
                <version>${amps.version}</version>
                <extensions>true</extensions>
                <configuration>
                <productVersion>${refapp.version}</productVersion>
                <!--<instructions>-->
                    <!--<Import-Package>org.w3c.dom;version="0.0.0"</Import-Package>-->
                <!--</instructions>-->

                </configuration>
            </plugin>
            <plugin>
                <artifactId>maven-compiler-plugin</artifactId>
                <configuration>
                    <source>1.6</source>
                    <target>1.6</target>
                </configuration>
            </plugin>
        </plugins>
    </build>
    <properties>
        <refapp.version>2.20.0</refapp.version>
        <amps.version>4.2.9</amps.version>

        <unity.portal.name>Unity Portal</unity.portal.name>
        <unity.portal.version>1.0.0</unity.portal.version>

        <plugin.testrunner.version>1.1.1</plugin.testrunner.version>
        <rest.version>2.8.2</rest.version>
        <soy.version>2.1.0</soy.version>
        <soy.compiler.version>1.5</soy.compiler.version>
        <spring.version>2.5.6.SEC01</spring.version>
    </properties>
</project>

When I add dependency to dom4j a have following error:

This XML file does not appear to have any style information associated with it. The document tree is shown below.
<status>
<status-code>500</status-code>
<message>Unable to configure EntityManagerFactory</message>
<stack-trace>
javax.persistence.PersistenceException: Unable to configure EntityManagerFactory
 at org.hibernate.ejb.Ejb3Configuration.configure(Ejb3Configuration.java:385)
 at org.hibernate.ejb.HibernatePersistence.createEntityManagerFactory(HibernatePersistence.java:56)
 at javax.persistence.Persistence.createEntityManagerFactory(Persistence.java:63)
 at com.honeywell.act.unity.um.rest.TestResource.testOrm(TestResource.java:75)
 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
 at java.lang.reflect.Method.invoke(Method.java:597)
 at com.atlassian.plugins.rest.common.interceptor.impl.DispatchProviderHelper$TypeOutInvoker$1.invoke(DispatchProviderHelper.java:205)
 at com.atlassian.plugins.rest.common.interceptor.impl.DispatchProviderHelper$1.intercept(DispatchProviderHelper.java:100)
 at com.atlassian.plugins.rest.common.interceptor.impl.DefaultMethodInvocation.invoke(DefaultMethodInvocation.java:61)
 at com.atlassian.plugins.rest.common.expand.interceptor.ExpandInterceptor.intercept(ExpandInterceptor.java:38)
 at com.atlassian.plugins.rest.common.interceptor.impl.DefaultMethodInvocation.invoke(DefaultMethodInvocation.java:61)
 at com.atlassian.plugins.rest.common.interceptor.impl.DispatchProviderHelper.invokeMethodWithInterceptors(DispatchProviderHelper.java:132)
 at com.atlassian.plugins.rest.common.interceptor.impl.DispatchProviderHelper$TypeOutInvoker._dispatch(DispatchProviderHelper.java:201)
 at com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(ResourceJavaMethodDispatcher.java:75)
 at com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.java:288)
 at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147)
 at com.sun.jersey.server.impl.uri.rules.ResourceClassRule.accept(ResourceClassRule.java:108)
 at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147)
 at com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootResourceClassesRule.java:84)
 at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1469)
 at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1400)
 at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1349)
 at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1339)
 at com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:416)
 at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:537)
 at com.atlassian.plugins.rest.module.RestDelegatingServletFilter$JerseyOsgiServletContainer.doFilter(RestDelegatingServletFilter.java:178)
 at com.sun.jersey.spi.container.servlet.ServletContainer.doFilter(ServletContainer.java:795)
 at com.atlassian.plugins.rest.module.RestDelegatingServletFilter.doFilter(RestDelegatingServletFilter.java:73)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:77)
 at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:63)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
 at com.atlassian.plugins.rest.module.servlet.RestServletUtilsUpdaterFilter.doFilterInternal(RestServletUtilsUpdaterFilter.java:26)
 at com.atlassian.plugins.rest.module.servlet.RestServletUtilsUpdaterFilter.doFilter(RestServletUtilsUpdaterFilter.java:40)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
 at com.atlassian.applinks.core.rest.context.ContextFilter.doFilter(ContextFilter.java:25)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
 at com.atlassian.prettyurls.filter.PrettyUrlsSiteMeshFixupFilter.doFilter(PrettyUrlsSiteMeshFixupFilter.java:36)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
 at com.atlassian.prettyurls.filter.PrettyUrlsDispatcherFilter.doFilter(PrettyUrlsDispatcherFilter.java:60)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
 at com.atlassian.prettyurls.filter.PrettyUrlsSiteMeshFilter.doFilter(PrettyUrlsSiteMeshFilter.java:92)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
 at com.atlassian.prettyurls.filter.PrettyUrlsMatcherFilter.doFilter(PrettyUrlsMatcherFilter.java:56)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
 at com.atlassian.labs.httpservice.resource.ResourceFilter.doFilter(ResourceFilter.java:59)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:77)
 at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:63)
 at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
 at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
 at com.opensymphony.sitemesh.webapp.SiteMeshFilter.obtainContent(SiteMeshFilter.java:129)
 at com.opensymphony.sitemesh.webapp.SiteMeshFilter.doFilter(SiteMeshFilter.java:77)
 at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
 at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:46)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
 at com.atlassian.prettyurls.filter.PrettyUrlsCombinedMatchDispatcherFilter.doFilter(PrettyUrlsCombinedMatchDispatcherFilter.java:61)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
 at com.atlassian.refapp.sal.ServletContextThreadLocalFilter.doFilter(ServletContextThreadLocalFilter.java:30)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:77)
 at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:63)
 at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
 at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:46)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
 at com.atlassian.refapp.auth.internal.AuthenticationContextCopyFilter.doFilter(AuthenticationContextCopyFilter.java:41)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
 at com.atlassian.seraph.filter.SecurityFilter.doFilter(SecurityFilter.java:219)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
 at com.atlassian.security.auth.trustedapps.filter.TrustedApplicationsFilter.doFilter(TrustedApplicationsFilter.java:100)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
 at com.atlassian.seraph.filter.BaseLoginFilter.doFilter(BaseLoginFilter.java:140)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
 at com.atlassian.oauth.serviceprovider.internal.servlet.OAuthFilter.doFilter(OAuthFilter.java:55)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
 at com.atlassian.plugins.rest.module.servlet.RestSeraphFilter.doFilter(RestSeraphFilter.java:44)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
 at com.atlassian.prettyurls.filter.PrettyUrlsCombinedMatchDispatcherFilter.doFilter(PrettyUrlsCombinedMatchDispatcherFilter.java:61)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:77)
 at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:63)
 at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
 at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:46)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
 at com.atlassian.refapp.decorator.PdlDarkToggleFilter.doFilter(PdlDarkToggleFilter.java:28)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
 at com.atlassian.fastdev.AutoReloadFilter.doFilter(AutoReloadFilter.java:63)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
 at com.atlassian.prettyurls.filter.PrettyUrlsCombinedMatchDispatcherFilter.doFilter(PrettyUrlsCombinedMatchDispatcherFilter.java:61)
 at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
 at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
 at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:77)
 at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:63)
 at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
 at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
 at com.atlassian.plugin.refimpl.webresource.RequestCacheCleaner.doFilter(RequestCacheCleaner.java:28)
 at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
 at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
 at com.atlassian.plugin.refimpl.filter.RefAppFirstFilter.doFilter(RefAppFirstFilter.java:32)
 at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
 at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
 at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
 at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
 at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:128)
 at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
 at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:567)
 at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
 at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:293)
 at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:849)
 at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:583)
 at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:454)
 at java.lang.Thread.run(Thread.java:662)
 Caused by: java.lang.ClassCastException: org.apache.xerces.jaxp.DocumentBuilderFactoryImpl cannot be cast to javax.xml.parsers.DocumentBuilderFactory
 at javax.xml.parsers.DocumentBuilderFactory.newInstance(Unknown Source)
 at org.hibernate.ejb.packaging.PersistenceXmlLoader.loadURL(PersistenceXmlLoader.java:89)
 at org.hibernate.ejb.packaging.PersistenceXmlLoader.deploy(PersistenceXmlLoader.java:171)
 at org.hibernate.ejb.Ejb3Configuration.configure(Ejb3Configuration.java:324)
 ... 152 more
</stack-trace>
</status>

I also tried to declare: 
<!--<instructions>-->
        <!--<Import-Package>org.w3c.dom;version="0.0.0"</Import-Package>-->
    <!--</instructions>-->

But then nothing worked (servlets, rest) -> error was 
com.atlassian.plugin.refimpl.servlet.NoOpServlet - [http-5990-1] - NoOpServlet received an unexpected request.

T think that: OSGI doesn't load org.w3c.dom and thats my problem. But I'm not sure.

Thanks
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