deech

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Apr 12, 2010, 5:29:07 PM4/12/10

to xnat_discussion

Hi all,
Just wanted to report on an issue with installing XNAT 1.4 on Ubuntu.
I installed tomcat6 using 'apt-get install tomcat6' and followed the
other install instructions on the XNAT wiki [1]. However accessing
localhost:8080/xnat/ got me a "HTTP 404- Requested Resource Is Not
Available" error.

Here's the corresponding error in /var/log/tomcat6/
localhost.<date>.log:
Apr 12, 2010 4:09:50 PM org.apache.catalina.core.ApplicationContext
log
INFO: SessionListener: contextDestroyed()
Apr 12, 2010 4:09:50 PM org.apache.catalina.core.ApplicationContext
log
INFO: ContextListener: contextDestroyed()
Apr 12, 2010 4:09:56 PM org.apache.catalina.core.ApplicationContext
log
INFO: ContextListener: contextInitialized()
Apr 12, 2010 4:09:56 PM org.apache.catalina.core.ApplicationContext
log
INFO: SessionListener: contextInitialized()
Apr 12, 2010 4:09:56 PM org.apache.catalina.core.StandardContext
listenerStart
SEVERE: Error configuring application listener of class
org.apache.axis.transport.http.AxisHTTPSessionListener
java.lang.ExceptionInInitializerError
at
org.apache.commons.discovery.jdk.JDKHooks.<clinit>(JDKHooks.java:75)
at
org.apache.commons.discovery.tools.DiscoverSingleton.find(DiscoverSingleton.java:
412)
at
org.apache.commons.discovery.tools.DiscoverSingleton.find(DiscoverSingleton.java:
378)
at org.apache.axis.components.logger.LogFactory
$1.run(LogFactory.java:45)
at java.security.AccessController.doPrivileged(Native Method)
at
org.apache.axis.components.logger.LogFactory.getLogFactory(LogFactory.java:
41)
at
org.apache.axis.components.logger.LogFactory.<clinit>(LogFactory.java:
33)
at
org.apache.axis.transport.http.AxisHTTPSessionListener.<clinit>(AxisHTTPSessionListener.java:
33)
at
sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at
sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:
39)
at
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:
27)
at java.lang.reflect.Constructor.newInstance(Constructor.java:
513)
at java.lang.Class.newInstance0(Class.java:355)
at java.lang.Class.newInstance(Class.java:308)
at
org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:
3878)
at
org.apache.catalina.core.StandardContext.start(StandardContext.java:
4429)
at
org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:
791)
at org.apache.catalina.core.ContainerBase.access
$000(ContainerBase.java:123)
at org.apache.catalina.core.ContainerBase
$PrivilegedAddChild.run(ContainerBase.java:145)
at java.security.AccessController.doPrivileged(Native Method)
at
org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:
769)
at
org.apache.catalina.core.StandardHost.addChild(StandardHost.java:526)
at
org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:902)
at
org.apache.catalina.startup.HostConfig.deployWARs(HostConfig.java:740)
at
org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:500)
at
org.apache.catalina.startup.HostConfig.start(HostConfig.java:1258)
at
org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:
321)
at
org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:
119)
at
org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1053)
at
org.apache.catalina.core.StandardHost.start(StandardHost.java:722)
at
org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1045)
at
org.apache.catalina.core.StandardEngine.start(StandardEngine.java:443)
at
org.apache.catalina.core.StandardService.start(StandardService.java:
516)
at
org.apache.catalina.core.StandardServer.start(StandardServer.java:710)
at org.apache.catalina.startup.Catalina.start(Catalina.java:
583)
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 org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:
288)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:
39)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:
25)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:
25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:
288)
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
org.apache.commons.daemon.support.DaemonLoader.start(DaemonLoader.java:
177)
Caused by: java.security.AccessControlException: access denied
(java.lang.RuntimePermission createClassLoader)
at
java.security.AccessControlContext.checkPermission(AccessControlContext.java:
323)
at
java.security.AccessController.checkPermission(AccessController.java:
546)
at
java.lang.SecurityManager.checkPermission(SecurityManager.java:532)
at
java.lang.SecurityManager.checkCreateClassLoader(SecurityManager.java:
594)
at java.lang.ClassLoader.<init>(ClassLoader.java:226)
at
org.apache.commons.discovery.jdk.PsuedoSystemClassLoader.<init>(PsuedoSystemClassLoader.java:
73)
at
org.apache.commons.discovery.jdk.JDK12Hooks.findSystemClassLoader(JDK12Hooks.java:
215)
at
org.apache.commons.discovery.jdk.JDK12Hooks.<clinit>(JDK12Hooks.java:
73)
... 45 more
Apr 12, 2010 4:09:56 PM org.apache.catalina.core.StandardContext
listenerStart
SEVERE: Skipped installing application listeners due to previous
error(s)

This is caused by tomcat not letting the jvm run certain methods, like
createClassLoader. In order to allow tomcat to run these methods I
appended the following block to the end of /etc/tomcat6/policy.d/
03catalina.policy:
grant codeBase "file:${catalina.base}/webapps/-" {
permission java.security.AllPermission;
};

This grants total access to all apps under the CATALINA_BASE/webapps
which in the standard Ubuntu install defaults to /var/lib/tomcat6/
webapps/.

Hope this helps,
-deech

[1] http://nrg.wikispaces.com/XNAT+Installation+Guide

Dan Ginsburg

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Apr 14, 2010, 2:15:15 PM4/14/10

to xnat_discussion

I installed XNAT 1.4 under Ubuntu 9.10 for the first time yesterday
and encountered the same issue. Thank you for posting this solution,
I had spent several hours debugging the issue. If it has not been
already, it would be good to add this to the installation guide on the
Wiki.

Thanks.

-- Dan

Timothy Olsen

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Apr 14, 2010, 2:57:53 PM4/14/10

to xnat_di...@googlegroups.com

Thank you deech and Dan. I've updated the Installation Guide with a warning about this potential issue.

Tim

Thanks.

-- Dan

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Herrick, Rick

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Jan 11, 2013, 1:01:25 PM1/11/13

to xnat_di...@googlegroups.com

Just to clarify, are you seeing the same error in your localhost log?

From: xnat_di...@googlegroups.com [mailto:xnat_di...@googlegroups.com] On Behalf Of Dominique Jennings
Sent: Friday, January 11, 2013 11:28 AM
To: xnat_di...@googlegroups.com
Cc: aditya...@gmail.com
Subject: [XNAT Discussion] Re: [SOLVED] Installation Error: HTTP 404 - Requested Resource Not Found

Hi all,

I have run into the same issue. I've installed apache tomcat 6.0.36, postgresql 9.2 and xnat 1.6 according to the instructions for xnat 1.6. At step 11 ("Start the webapp and login"), I point my browser to http://localhost:8080/xnat, and I get the 404 error.

I've uncommented:

grant codeBase "file:${catalina.base}/webapps/-" {

permission java.security.AllPermission;

as described by deech below. I'm doing this on a Mac OS X 10.7.5.

If anyone can help, I would be eternally grateful.

Thanks in advance.

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Dominique Jennings

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Jan 11, 2013, 3:07:42 PM1/11/13

to xnat_di...@googlegroups.com

No, I'm not. Here's my (incomprehensible to me) localhost log output from /usr/local/apache-tomcat-6.0.36/logs/localhost.2013-01-11.log:

--------------------------

Jan 11, 2013 9:08:25 AM org.apache.catalina.core.ApplicationContext log

INFO: Destroying Spring FrameworkServlet 'spring-mvc'

Jan 11, 2013 9:08:28 AM org.apache.catalina.core.ApplicationContext log

INFO: SessionListener: contextDestroyed()

Jan 11, 2013 9:08:28 AM org.apache.catalina.core.ApplicationContext log

INFO: ContextListener: contextDestroyed()

Jan 11, 2013 9:18:12 AM org.apache.catalina.core.ApplicationContext log

INFO: Initializing Spring FrameworkServlet 'spring-mvc'

Jan 11, 2013 9:18:25 AM org.apache.catalina.core.ApplicationContext log

INFO: ContextListener: contextInitialized()

Jan 11, 2013 9:18:25 AM org.apache.catalina.core.ApplicationContext log

INFO: SessionListener: contextInitialized()

Jan 11, 2013 11:02:46 AM org.apache.catalina.core.ApplicationContext log

INFO: Initializing Spring FrameworkServlet 'spring-mvc'

Jan 11, 2013 11:03:08 AM org.apache.catalina.core.ApplicationContext log

SEVERE: StandardWrapper.Throwable

java.lang.RuntimeException: unable to start DICOM SCP

at org.nrg.dcm.DicomSCPManager.startOrStopDicomSCPAsDictatedByConfiguration(DicomSCPManager.java:32)

at org.nrg.xnat.restlet.servlet.XNATRestletServlet.init(XNATRestletServlet.java:93)

at javax.servlet.GenericServlet.init(GenericServlet.java:212)

at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1206)

at org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:1026)

at org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:4421)

at org.apache.catalina.core.StandardContext.start(StandardContext.java:4734)

at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:799)

at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:779)

at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:601)

at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:943)

at org.apache.catalina.startup.HostConfig.deployWARs(HostConfig.java:778)

at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:504)

at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1317)

at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:324)

at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:142)

at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1065)

at org.apache.catalina.core.StandardHost.start(StandardHost.java:840)

at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1057)

at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:463)

at org.apache.catalina.core.StandardService.start(StandardService.java:525)

at org.apache.catalina.core.StandardServer.start(StandardServer.java:754)

at org.apache.catalina.startup.Catalina.start(Catalina.java:595)

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 org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:289)

at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:414)

Caused by: java.net.BindException: Address already in use

at java.net.PlainSocketImpl.socketBind(Native Method)

at java.net.PlainSocketImpl.bind(PlainSocketImpl.java:383)

at java.net.ServerSocket.bind(ServerSocket.java:328)

at org.dcm4che2.net.NetworkConnection.bind(NetworkConnection.java:630)

at org.dcm4che2.net.Device.startListening(Device.java:711)

at org.nrg.dcm.DicomSCP.start(DicomSCP.java:306)

at org.nrg.dcm.DicomSCPManager.startOrStopDicomSCPAsDictatedByConfiguration(DicomSCPManager.java:24)

... 28 more

Jan 11, 2013 11:03:08 AM org.apache.catalina.core.StandardContext loadOnStartup

SEVERE: Servlet /xnat threw load() exception

java.net.BindException: Address already in use