Install step 8: No authentication.properties file found in conf directory. Skipping enhanced authentication method.

John McLean

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Nov 15, 2012, 10:48:57 AM11/15/12

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Hi,

Having toiled with and finally got past install steps 1 to 4 I now feel I'm on the downhill slope. However, I got the following error when running step 8 of the install process. I'm a little unsure if it is signifcant or not and whether I can just soldier on and deploy the webapp. The command and error are as follows:

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

StoreXML -dir ./work/field_groups -u admin -p admin_pswd -allowDataDeletion true

No authentication.properties file found in conf directory. Skipping enhanced authentication method.

Found Document: /home/xnat/xnat_1_6_builder/deployments/quic/./work/field_groups/1.xml

Error: No username and password.

ERROR: See log for details (logs/xdat.log).

Error: No username and password.

ERROR: See log for details (logs/xdat.log).

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

As far as I'm aware I haven't set the admin username or password yet (or have I), I take it these are distinct from the xdat.project.user and xdat.project.password defined in build.properties?

As you can see from my command above i kept admin as the username but I changed the password from the default, maybe I shouldn't have done this and i should stick with admin / admin and adjust later?

Any guidance would be a big help and is much appreciated

Thanks

John

Herrick, Rick

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Nov 15, 2012, 11:07:50 AM11/15/12

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The authentication.properties warning is completely meaningless. Don’t worry about that.

The admin/admin password is actually set up in step 7 prior to the XML import of the field groups:

StoreXML -project PROJECT_NAME -l security/security.xml -allowDataDeletion true

That creates the admin and guest user accounts.

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John McLean

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Nov 15, 2012, 11:09:28 AM11/15/12

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Here is some further info related to my previous post which may be useful for debugging.

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

[xnat@xnat1 logs]$ cat xdat.log | grep admin

[xnat@xnat1 logs]$ cat xdat.log | grep username

java.lang.Exception: Error: No username and password.

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

[xnat@xnat1 logs]$ echo $JAVA_HOME

/usr/java/jdk1.7.0_07

NB but this doesnt necessarily refer to tomcat specifically

[xnat@xnat1 logs]$ tomcat6 version

Error: Could not find or load main class org.apache.catalina.util.ServerInfo

locate catalina.sh

/opt/dell/srvadmin/lib64/openmanage/apache-tomcat/bin/catalina.sh

i.e. to find out which version of java tomcat is using...

see webpage below for help...

http://stackoverflow.com/questions/5957851/how-do-i-find-what-java-version-tomcat6-is-using

vi /opt/dell/srvadmin/lib64/openmanage/apache-tomcat/bin/catalina.sh

but my java version looks like i am using jdk? :

[xnat@xnat1 logs]$ java -version

java version "1.6.0_24"

OpenJDK Runtime Environment (IcedTea6 1.11.4) (rhel-1.49.1.11.4.el6_3-x86_64)

OpenJDK 64-Bit Server VM (build 20.0-b12, mixed mode)

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

Hope that helps to some degree

Thanks

John

John

John McLean

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Nov 15, 2012, 11:12:57 AM11/15/12

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Thanks Rick,

I posted some more info so please ignore.

So am I free to define a different admin username and password in step 8 or do I have to stick with admin/admin if that was set in step 7 ?

Thanks again

John

Herrick, Rick

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Nov 15, 2012, 11:27:59 AM11/15/12

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You have to stick with admin/admin for the installation OR you can change the values set in the security.xml file referenced in the StoreXML command. What most people do is just use admin/admin to get the system bootstrapped, then log in with that account, create a new admin account with a different name and a sound password, then deactivate the default admin account. If you’ve already run step 7, then you’ve got the admin account set up, so I’d just go with that, meaning that in step 8 the –u and –p options both take the value admin. Once the server’s up and going, log in as admin/admin, go to Administer->Users, create a new admin user (e.g. jmcleanAdmin), log out, log back in with your new admin account, and deactivate the default admin account.

Of course, if you’re just setting up a development instance to tinker with, you’re fine leaving the default admin account on there for ease of use. Anything accessible to the outside or with real research data should be better secured however.

Roman Valls Guimerà

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Sep 18, 2014, 10:22:16 AM9/18/14

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Hello Rick,

Back to the future (from 2012-11-15), I am having this exact same problem (cmdline complaining on StoreXML), but I'm also unable to login using admin/admin via the web interface on localhost:8080/xnat :-/

I'm getting the following from the webapp logs (located under "/var/lib/tomcat6/webapps/xnat/logs"):

2014-09-18 14:19:14,696 [org.springframework.scheduling.quartz.SchedulerFactoryBean#0_Worker-1] ERROR org.nrg.xnat.utils.XnatUserProvider - Unable to retrieve user admin

org.nrg.xdat.security.XDATUser$UserNotFoundException: Invalid Login and/or Password

at org.nrg.xdat.security.XDATUser.<init>(XDATUser.java:119)

at org.nrg.xnat.utils.XnatUserProvider.get(XnatUserProvider.java:35)

at org.nrg.xnat.utils.XnatUserProvider.get(XnatUserProvider.java:19)

at org.nrg.xnat.helpers.prearchive.SessionXMLRebuilderJob.execute(SessionXMLRebuilderJob.java:40)

at org.nrg.schedule.DelegatingJobBean.executeInternal(DelegatingJobBean.java:55)

at org.springframework.scheduling.quartz.QuartzJobBean.execute(QuartzJobBean.java:86)

at org.quartz.core.JobRunShell.run(JobRunShell.java:216)

at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:549)

2014-09-18 14:20:13,246 [org.springframework.scheduling.quartz.SchedulerFactoryBean#0_Worker-6] ERROR org.nrg.xnat.utils.XnatUserProvider - Unable to retrieve user admin

org.nrg.xdat.security.XDATUser$UserNotFoundException: Invalid Login and/or Password

at org.nrg.xdat.security.XDATUser.<init>(XDATUser.java:119)

at org.nrg.xnat.utils.XnatUserProvider.get(XnatUserProvider.java:35)

at org.nrg.xnat.utils.XnatUserProvider.get(XnatUserProvider.java:19)

at org.nrg.xnat.helpers.prearchive.SessionXMLRebuilderJob.execute(SessionXMLRebuilderJob.java:40)

at org.nrg.schedule.DelegatingJobBean.executeInternal(DelegatingJobBean.java:55)

at org.springframework.scheduling.quartz.QuartzJobBean.execute(QuartzJobBean.java:86)

at org.quartz.core.JobRunShell.run(JobRunShell.java:216)

at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:549)

The exact steps I followed to setup the instance are here:

https://github.com/brainstorm/ansible-xnat/blob/master/roles/xnat/tasks/main.yml

Where should I poke to get this initial user/role working and letting me login?

Thanks!

PD: Now the ansible-xnat playbook should be fully deployable now on localhost, I just fixed a couple of bugs with the java/tomcat6 roles (dependencies):

git clone https://github.com/brainstorm/ansible-xnat.git && cd ansible-xnat && vagrant up

(after installing virtualbox and vagrant)

Herrick, Rick

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Sep 18, 2014, 10:33:49 AM9/18/14

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I would suggest completely dropping the database at this point. It’s pretty clear you don’t have the admin role in the database, so it’s hard to guess what state it’s in. I’d GUESS (OK, so it’s not so hard to guess; but it would be hard to bet, as in, this guess is worth as much as you’ve paid for it J ) that you have the database schema installed but no data in it. So you could probably run StoreXML, get your security set-up initialized, and you’d be fine. But I’m not sure about that and it’s fairly easy to drop the database, re-create the database, and re-run the database script to initialize the schema. So it’d be something like this:

dropdb –U xnat xnat

createdb –U xnat xnat

psql –U xnat –f sql/xnat.sql

StoreXML -l security/security.xml -allowDataDeletion true

A couple notes on this:

· Make certain that Tomcat is not running during any of this, but especially not when you are running StoreXML (actually, you probably wouldn’t be able to drop the database if Tomcat was running).

· The “No authentication.properties file…” warning is nothing to worry about. It’s a standard message from one of the libraries as it tries to see if you have set up something to override the default authentication method.

Give that a try and let me know how it turns out.

I’m pretty psyched on the ansible-xnat playbook. We’ll pull it and test it out here real soon!

Rick Herrick

Sr. Programmer/Analyst

Neuroinformatics Research Group

Washington University School of Medicine

(314) 827-4250

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Roman Valls Guimerà

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Sep 18, 2014, 12:03:57 PM9/18/14

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Apparently the following did the trick as you suggested (still not sure why though since I think I followed the docs faithfully in "tasks/main.yml' :-/):

root@localhost:/home/vagrant# su - xnat -c "dropdb -U xnat xnat"

root@localhost:/home/vagrant# su - xnat -c "createdb -U xnat xnat"

root@localhost:/home/vagrant# su - xnat -c "psql -U xnat -f /usr/local/xnat/deployments/xnat/sql/xnat.sql"

root@localhost:/home/vagrant# cd /usr/local/xnat/deployments/xnat/

root@localhost:/usr/local/xnat/deployments/xnat# /usr/local/xnat/bin/StoreXML -l security/security.xml -allowDataDeletion true

root@localhost:/usr/local/xnat# source bin/setenv.sh && bin/update.sh -Ddeploy=true

But anyway, I'm facing more issues now after successfully authenticating as admin/admin:

An error has occurred.

Please contact your IT staff or the application logs for more information.

Logs show up:

2014-09-18 15:55:44,584 [main] ERROR velocity - VM #xdatStringBoxOnChange: error : too few arguments to macro. Wanted 6 got 0

2014-09-18 15:55:44,774 [main] ERROR velocity - VM #xdatSearchForm: error : too few arguments to macro. Wanted 2 got 0

2014-09-18 15:55:45,017 [main] ERROR velocity - VM #displayFileSystem: error : too few arguments to macro. Wanted 1 got 0

2014-09-18 15:55:45,020 [main] ERROR velocity - VM #auditBoxes: error : too few arguments to macro. Wanted 4 got 0

2014-09-18 15:56:11,771 [http-8983-4] ERROR velocity - Left side ($sessionCount) of '>' operation has null value. Operation not possible. navigations//DefaultTop.vm [line 157, column 21]

2014-09-18 15:56:11,771 [http-8983-4] ERROR velocity - Left side ($sessionIpCount) of '>' operation has null value. Operation not possible. navigations//DefaultTop.vm [line 157, column 44]

2014-09-18 15:56:11,604 [http-8983-4] ERROR org.apache.turbine.Turbine - Turbine.handleException:

java.lang.ClassNotFoundException:

Requested Page not found: Default

Turbine looked in the following modules.packages path:

[org.apache.turbine.app.xnat.modules, org.nrg.xnat.turbine.modules, org.nrg.xdat.turbine.modules, org.apache.turbine.app.xnat.modules, org.apache.turbine.modules]

at org.apache.turbine.modules.PageLoader.getInstance(PageLoader.java:169)

at org.apache.turbine.modules.PageLoader.exec(PageLoader.java:98)

at org.apache.turbine.Turbine.doGet(Turbine.java:751)

at javax.servlet.http.HttpServlet.service(HttpServlet.java:617)

at javax.servlet.http.HttpServlet.service(HttpServlet.java:723)

But those might be more related to the fact that I'm running OpenJDK-7 instead of Oracle's? Will replace JDK's tomorrow, but in any case, ping me if you see something clearly wrong in my playbook (out of order, etc...):

https://github.com/brainstorm/ansible-xnat/blob/master/roles/xnat/tasks/main.yml

Thanks Rick!

Roman

Roman Valls Guimerà

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Sep 19, 2014, 5:43:00 AM9/19/14

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This backtrace is quite suspicious...:

org.springframework.beans.factory.BeanDefinitionStoreException: Unexpected exception parsing XML document from ServletContext resource [/WEB-INF/conf/xnat-security.xml]; nested exception is java.lang.InternalError: internal error: SeedGenerator thread generated an exception.

at org.springframework.beans.factory.xml.XmlBeanDefinitionReader.doLoadBeanDefinitions(XmlBeanDefinitionReader.java:412)

at org.springframework.beans.factory.xml.XmlBeanDefinitionReader.loadBeanDefinitions(XmlBeanDefinitionReader.java:334)

at org.springframework.beans.factory.xml.XmlBeanDefinitionReader.loadBeanDefinitions(XmlBeanDefinitionReader.java:302)

at org.springframework.beans.factory.support.AbstractBeanDefinitionReader.loadBeanDefinitions(AbstractBeanDefinitionReader.java:143)

at org.springframework.beans.factory.support.AbstractBeanDefinitionReader.loadBeanDefinitions(AbstractBeanDefinitionReader.java:178)

at org.springframework.beans.factory.support.AbstractBeanDefinitionReader.loadBeanDefinitions(AbstractBeanDefinitionReader.java:149)

at org.springframework.web.context.support.XmlWebApplicationContext.loadBeanDefinitions(XmlWebApplicationContext.java:124)

at org.springframework.web.context.support.XmlWebApplicationContext.loadBeanDefinitions(XmlWebApplicationContext.java:93)

at org.springframework.context.support.AbstractRefreshableApplicationContext.refreshBeanFactory(AbstractRefreshableApplicationContext.java:130)

at org.springframework.context.support.AbstractApplicationContext.obtainFreshBeanFactory(AbstractApplicationContext.java:467)

at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:397)

at org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:467)

at org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:483)

at org.springframework.web.servlet.FrameworkServlet.initWebApplicationContext(FrameworkServlet.java:358)

at org.springframework.web.servlet.FrameworkServlet.initServletBean(FrameworkServlet.java:325)

at org.springframework.web.servlet.HttpServletBean.init(HttpServletBean.java:127)

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

at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1213)

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

at org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:4425)

at org.apache.catalina.core.StandardContext.start(StandardContext.java:4738)

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:583)

at org.apache.catalina.startup.HostConfig.deployDirectory(HostConfig.java:1079)

at org.apache.catalina.startup.HostConfig.deployDirectories(HostConfig.java:1002)

at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:506)

at org.apache.catalina.startup.HostConfig.check(HostConfig.java:1385)

at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:306)

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

at org.apache.catalina.core.ContainerBase.backgroundProcess(ContainerBase.java:1389)

at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1653)

at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.processChildren(ContainerBase.java:1662)

at org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor.run(ContainerBase.java:1642)

at java.lang.Thread.run(Thread.java:745)

Caused by: java.lang.InternalError: internal error: SeedGenerator thread generated an exception.

at sun.security.provider.SeedGenerator$ThreadedSeedGenerator.getSeedByte(SeedGenerator.java:394)

at sun.security.provider.SeedGenerator$ThreadedSeedGenerator.getSeedBytes(SeedGenerator.java:379)

at sun.security.provider.SeedGenerator.generateSeed(SeedGenerator.java:139)

at sun.security.provider.SecureRandom$SeederHolder.<clinit>(SecureRandom.java:186)

at sun.security.provider.SecureRandom.engineNextBytes(SecureRandom.java:203)

at java.security.SecureRandom.nextBytes(SecureRandom.java:455)

at java.security.SecureRandom.next(SecureRandom.java:477)

at java.util.Random.nextLong(Random.java:334)

at org.springframework.security.config.http.AuthenticationConfigBuilder.createKey(AuthenticationConfigBuilder.java:402)

at org.springframework.security.config.http.AuthenticationConfigBuilder.createAnonymousFilter(AuthenticationConfigBuilder.java:380)

at org.springframework.security.config.http.HttpSecurityBeanDefinitionParser.parse(HttpSecurityBeanDefinitionParser.java:106)

at org.springframework.security.config.SecurityNamespaceHandler.parse(SecurityNamespaceHandler.java:86)

at org.springframework.beans.factory.xml.BeanDefinitionParserDelegate.parseCustomElement(BeanDefinitionParserDelegate.java:1338)

at org.springframework.beans.factory.xml.BeanDefinitionParserDelegate.parseCustomElement(BeanDefinitionParserDelegate.java:1328)

at org.springframework.beans.factory.xml.DefaultBeanDefinitionDocumentReader.parseBeanDefinitions(DefaultBeanDefinitionDocumentReader.java:135)

at org.springframework.beans.factory.xml.DefaultBeanDefinitionDocumentReader.registerBeanDefinitions(DefaultBeanDefinitionDocumentReader.java:93)

at org.springframework.beans.factory.xml.XmlBeanDefinitionReader.registerBeanDefinitions(XmlBeanDefinitionReader.java:493)

at org.springframework.beans.factory.xml.XmlBeanDefinitionReader.doLoadBeanDefinitions(XmlBeanDefinitionReader.java:390)

... 34 more

Roman Valls Guimerà

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Sep 19, 2014, 5:52:25 AM9/19/14

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Upgraded to Oracle's Java7, same issues, another exception I missed before seemingly related to auth:

2014-09-19 09:49:15,434 [http-8983-4] ERROR org.apache.turbine.Turbine - Turbine.handleException:

java.lang.ClassNotFoundException:

Requested Page not found: Default

Turbine looked in the following modules.packages path:

[org.apache.turbine.app.xnat.modules, org.nrg.xnat.turbine.modules, org.nrg.xdat.turbine.modules, org.apache.turbine.app.xnat.modules, org.apache.turbine.modules]

at org.apache.turbine.modules.PageLoader.getInstance(PageLoader.java:169)

at org.apache.turbine.modules.PageLoader.exec(PageLoader.java:98)

at org.apache.turbine.Turbine.doGet(Turbine.java:751)

at javax.servlet.http.HttpServlet.service(HttpServlet.java:617)

at javax.servlet.http.HttpServlet.service(HttpServlet.java:723)

at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)

at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)

at net.bull.javamelody.MonitoringFilter.doFilter(MonitoringFilter.java:206)

at net.bull.javamelody.MonitoringFilter.doFilter(MonitoringFilter.java:179)

at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)

at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)

at org.nrg.xnat.restlet.util.UpdateExpirationCookie.doFilter(UpdateExpirationCookie.java:38)

at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)

at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)

at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:369)

at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:109)

at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:83)