Possible 1.4.2 bugs

16 views

Skip to first unread message

Alex

unread,

Feb 3, 2011, 9:07:49 PM2/3/11

to xnat_discussion

I'm testing 1.4.2 that was upgraded from 1.4rc3 with a copy of the
original database. I came across a few problems that might be bugs,
please see below for description and screen captures.

1. When I go to unassigned prearchive and click on a study link, it
takes me to session detail. Instead of project name combo box, it
shows: $om.getProject($project,false).getDisplayID()
https://docs.google.com/leaf?id=0B5EqZ7UllzwSNDRlZTZkNTYtY2ZkYy00N2E3LTlkNTYtZjVlYjJmMzFhZTVj&hl=en&authkey=CJ6ZwacI

2. When I go to Advanced Search, the Select Pivot Data-type to search
combo box is empty.
https://docs.google.com/leaf?id=0B5EqZ7UllzwSN2YxNTI1OWItYzhlZC00ODI0LTgzY2MtNzRlYWQ2M2MyNGU4&hl=en&authkey=COrOxbMC

3. When I pick one of the projects off the main page, it displays just
the top tab panel (Details, Access...), but not the lower tab panel
(Subjects and so on). That happens only in one of the projects.
https://docs.google.com/leaf?id=0B5EqZ7UllzwSYzZlN2E1ZDItZWM2NS00ZDlmLTkyZTYtMmU1M2MxNTQxNTkx&hl=en&authkey=CNz15cQN

Any ideas on how to fix these?

Thanks, Alex.

Alexis

unread,

Feb 11, 2011, 3:19:46 AM2/11/11

to xnat_discussion

Dear Alex,

I don't have a precise answer to your problems, however I'm confident
you have a general problem to fix with the security settings.
Additionally to the points you mentioned, I see on all your sreenshots
that in the left panel, the "Data" item cannot be expanded. So unless
you don't have any data stored, which can mean you don't have the
rights to see the data ( but it doesn't tell us if this is at the
project level or at the datatype level ).
One first check you be to go to "Administer" -> "Datatypes", and see
if the datatype list is not empty.
Also you could try to go to "Administer" -> "More Options" and "Clear
DB cache", and maybe also the reload settings options.
If nothing fix the problem, you could try to create a new project and
store data in it, and see if you can browse it.

Alexis

On 3 fév, 21:07, Alex <skiz...@gmail.com> wrote:
> I'm testing 1.4.2 that was upgraded from 1.4rc3 with a copy of the
> original database. I came across a few problems that might be bugs,
> please see below for description and screen captures.
>
> 1. When I go to unassigned prearchive and click on a study link, it
> takes me to session detail. Instead of project name combo box, it

> shows: $om.getProject($project,false).getDisplayID()https://docs.google.com/leaf?id=0B5EqZ7UllzwSNDRlZTZkNTYtY2ZkYy00N2E3...

>
> 2. When I go to Advanced Search, the Select Pivot Data-type to search

> combo box is empty.https://docs.google.com/leaf?id=0B5EqZ7UllzwSN2YxNTI1OWItYzhlZC00ODI0...

>
> 3. When I pick one of the projects off the main page, it displays just
> the top tab panel (Details, Access...), but not the lower tab panel

> (Subjects and so on). That happens only in one of the projects.https://docs.google.com/leaf?id=0B5EqZ7UllzwSYzZlN2E1ZDItZWM2NS00ZDlm...

Alex

unread,

Feb 15, 2011, 4:55:07 PM2/15/11

to xnat_discussion

Hi Alexis,

Thank you for your suggestions.

I tried all the options you suggested but that didn't resolve my
problem.

> One first check you be to go to "Administer" -> "Datatypes", and see
> if the datatype list is not empty.

Datatypes were there.

> Also you could try to go to "Administer" -> "More Options" and "Clear
> DB cache", and maybe also the reload settings options.

Clear DB cache, no changes.

> If nothing fix the problem, you could try to create a new project and
> store data in it, and see if you can browse it.

I was able to create a new project.

I'm still looking into this issue.

Thanks, Alex.

Alex

unread,

Feb 16, 2011, 8:10:33 PM2/16/11

to xnat_discussion

Sorry for bumping this, but are there any more suggestions about these
issues in 1.4.2?

On Feb 3, 9:07 pm, Alex <skiz...@gmail.com> wrote:
> I'm testing 1.4.2 that was upgraded from 1.4rc3 with a copy of the
> original database. I came across a few problems that might be bugs,
> please see below for description and screen captures.
>
> 1. When I go to unassigned prearchive and click on a study link, it
> takes me to session detail. Instead of project name combo box, it

> shows: $om.getProject($project,false).getDisplayID()https://docs.google.com/leaf?id=0B5EqZ7UllzwSNDRlZTZkNTYtY2ZkYy00N2E3...

>
> 2. When I go to Advanced Search, the Select Pivot Data-type to search

> combo box is empty.https://docs.google.com/leaf?id=0B5EqZ7UllzwSN2YxNTI1OWItYzhlZC00ODI0...

>
> 3. When I pick one of the projects off the main page, it displays just
> the top tab panel (Details, Access...), but not the lower tab panel

> (Subjects and so on). That happens only in one of the projects.https://docs.google.com/leaf?id=0B5EqZ7UllzwSYzZlN2E1ZDItZWM2NS00ZDlm...

Olsen, Tim

unread,

Feb 17, 2011, 3:33:15 PM2/17/11

to xnat_di...@googlegroups.com

1. When I go to unassigned prearchive and click on a study link, it takes me to session detail. Instead of project name combo box, it
shows: $om.getProject($project,false).getDisplayID()
https://docs.google.com/leaf?id=0B5EqZ7UllzwSNDRlZTZkNTYtY2ZkYy00N2E3LTlkNTYtZjVlYjJmMzFhZTVj&hl=en&authkey=CJ6ZwacI

-- Is this for a session that was in the Unassigned folder? If not, I think it's a symptom of the problems you are seeing elsewhere.

2. When I go to Advanced Search, the Select Pivot Data-type to search combo box is empty.
https://docs.google.com/leaf?id=0B5EqZ7UllzwSN2YxNTI1OWItYzhlZC00ODI0LTgzY2MtNzRlYWQ2M2MyNGU4&hl=en&authkey=COrOxbMC

-- Are there any errors in the TOMCAT/webapps/xnat/logs/xdat.log or application.log?

3. When I pick one of the projects off the main page, it displays just the top tab panel (Details, Access...), but not the lower tab panel (Subjects and so on). That happens only in one of the projects.
https://docs.google.com/leaf?id=0B5EqZ7UllzwSYzZlN2E1ZDItZWM2NS00ZDlmLTkyZTYtMmU1M2MxNTQxNTkx&hl=en&authkey=CNz15cQN

-- Try going to the Edit Details page for that project and click submit without making modifications. This should reset the data-type permissions for the project.

Tim

The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

Alex

unread,

Feb 18, 2011, 2:46:40 PM2/18/11

to xnat_discussion

Tim,

On Feb 17, 3:33 pm, "Olsen, Tim" <ols...@mir.wustl.edu> wrote:
> 1. When I go to unassigned prearchive and click on a study link, it takes me to session detail. Instead of project name combo box, it

> shows: $om.getProject($project,false).getDisplayID()https://docs.google.com/leaf?id=0B5EqZ7UllzwSNDRlZTZkNTYtY2ZkYy00N2E3...

>
> -- Is this for a session that was in the Unassigned folder? If not, I think it's a symptom of the problems you are seeing elsewhere.

Yes, this happens for all sessions in the Unassigned folder.

>
> 2. When I go to Advanced Search, the Select Pivot Data-type to search combo box is empty.https://docs.google.com/leaf?id=0B5EqZ7UllzwSN2YxNTI1OWItYzhlZC00ODI0...

>
> -- Are there any errors in the TOMCAT/webapps/xnat/logs/xdat.log or application.log?
>

Nothing in the logs.

> 3. When I pick one of the projects off the main page, it displays just the top tab panel (Details, Access...), but not the lower tab panel (Subjects and so on). That happens only in one of the projects.https://docs.google.com/leaf?id=0B5EqZ7UllzwSYzZlN2E1ZDItZWM2NS00ZDlm...

>
> -- Try going to the Edit Details page for that project and click submit without making modifications. This should reset the data-type permissions for the project.

Tried changing access rules and submitting as well as submitting
without any changes - still no lower panel.

Thanks, Alex.

Olsen, Tim

unread,

Feb 18, 2011, 2:55:25 PM2/18/11

to xnat_di...@googlegroups.com

>Yes, this happens for all sessions in the Unassigned folder.

In order to archive sessions, they must be in a project folder. Archiving from the Unassigned folder is not allowed. Try moving the sessions to a proper project and reattempting the archive.

What happens if you login as a non-admin user who has access to that project? Do you see the listings then?

Tim

Tim,

Nothing in the logs.

Thanks, Alex.

--
You received this message because you are subscribed to the Google Groups "xnat_discussion" group.
To post to this group, send email to xnat_di...@googlegroups.com.
To unsubscribe from this group, send email to xnat_discussi...@googlegroups.com.
For more options, visit this group at http://groups.google.com/group/xnat_discussion?hl=en.

Alex

unread,

Feb 18, 2011, 3:43:37 PM2/18/11

to xnat_discussion

Same result with a non-admin user - no listing. This happens only for
one project as far as I can see. I'm wondering if the data in the
project is causing this.

> For more options, visit this group athttp://groups.google.com/group/xnat_discussion?hl=en.

Olsen, Tim

unread,

Feb 21, 2011, 12:44:14 PM2/21/11

to xnat_di...@googlegroups.com

If it was a problem with the actual data, I would expect to see something in the log. I suspect it might be a permission configuration issue.

When you view all subjects, (via the left bar -> Data -> Subjects) do subjects for this project show up?

When you view the pertinent project page, are there javascript errors reported?

Tim

For more options, visit this group at http://groups.google.com/group/xnat_discussion?hl=en.

Olsen, Tim

unread,

Mar 1, 2011, 5:22:14 PM3/1/11

to xnat_di...@googlegroups.com

Regarding the problematic project page, does the project ID for this project include any odd characters? What is the Project ID? We've had a similar bug on one of our servers.

Tim

-----Original Message-----
From: xnat_di...@googlegroups.com [mailto:xnat_di...@googlegroups.com] On Behalf Of Alex
Sent: Wednesday, February 16, 2011 7:11 PM
To: xnat_discussion
Subject: Re: Possible 1.4.2 bugs

Alex

unread,

Mar 1, 2011, 11:49:23 PM3/1/11

to xnat_discussion

The ID is "TP" (without quotes). Project title has an opening and a
closing parenthesis: "Test (Alex)" (without quotes). I tried changing
title to remove the parenthesis - that didn't help.

I'm running this instance (1.4.2) of XNAT in parallel to our
production XNAT. I noticed that the the logs in webapps/
<1.4.2_project_name>/logs are not updated for some reason. The logs in
the production XNAT are updated. I guess that's why I don't see any
errors in the logs. What could be the reason for that?

Alex.

> For more options, visit this group athttp://groups.google.com/group/xnat_discussion?hl=en.

Tim Olsen

unread,

Mar 2, 2011, 12:42:35 AM3/2/11

to xnat_discussion

The problem we had locally involved project IDs that started with
integers. Sounds like a different issue, though with similar effect.

There tends to be some log4j confusion when two XNATs are running on
the same server. We generally can avoid running two XNATs on the same
machine, so its been a low priority bug.

Are there any javascript errors on the page? The bottom tabs are
loaded via AJAX, if you view the Network or Resource traffic in
Firefox -> Firebug or Chrome -> Developer Tools does it notify you of
any issues? Any server calls returning a 500 status code?

Tim

Alex

unread,

Mar 2, 2011, 5:33:50 PM3/2/11

to xnat_discussion

I do not see any javascript errors or server errors in Chrome's
Developer Tools.

Here's a capture of XHR for a project that doesn't work:
http://goo.gl/iWlov

Here's one for a project that works:
http://goo.gl/wjB0d

Alex.

Olsen, Tim

unread,

Mar 3, 2011, 10:58:38 AM3/3/11

to xnat_di...@googlegroups.com

To go back a few emails, can you see the subjects or sessions when you view ALL using the data link on the left.

> When you view all subjects, (via the left bar -> Data -> Subjects) do subjects for this project show up?

Tim

Alex.

For more options, visit this group at http://groups.google.com/group/xnat_discussion?hl=en.

Alex

unread,

Mar 3, 2011, 1:22:30 PM3/3/11

to xnat_discussion

Data doesn't expand and when I click on Data nothing happens, no
javascript errors either.

Alex.

Olsen, Tim

unread,

Mar 3, 2011, 1:24:29 PM3/3/11

to xnat_di...@googlegroups.com

Ah. That's broken too. How about if you go to HOST/REST/experiments?format=html ?

Alex.

For more options, visit this group at http://groups.google.com/group/xnat_discussion?hl=en.

Alex

unread,

Mar 3, 2011, 2:05:34 PM3/3/11

to xnat_discussion

That gives me a list of experiment ids, project ids, date, xsiType,
label, insert date and URI.

Olsen, Tim

unread,

Mar 3, 2011, 2:19:05 PM3/3/11

to xnat_di...@googlegroups.com

Do the experiments for the affected project show up? If you do that URL as an admin account, you should see all experiments in your database.

Tim

For more options, visit this group at http://groups.google.com/group/xnat_discussion?hl=en.

Alex

unread,

Mar 3, 2011, 2:53:17 PM3/3/11

to xnat_discussion

I can see the affected project's experiments in the list.

Olsen, Tim

unread,

Mar 3, 2011, 3:29:19 PM3/3/11

to xnat_di...@googlegroups.com

I've seen issues similar to this on other upgrades. Its usually some odd configuration thing. Any chance I can get access to this website? Preferably a test version.

ols...@mir.wustl.edu

For more options, visit this group at http://groups.google.com/group/xnat_discussion?hl=en.

Alex

unread,

Mar 3, 2011, 4:21:39 PM3/3/11

to xnat_discussion, Olsen, Tim

I just sent you the information.

Olsen, Tim

unread,

Mar 9, 2011, 12:26:54 PM3/9/11

to xnat_di...@googlegroups.com

It looks like this project was created on a 1.4 RC version which had a permissions bug. Unfortunately, I think the clearest way to fix it is to do some light surgery on your database.

I detail the SQL that should be run here:

http://groups.google.com/group/xnat_discussion/browse_thread/thread/39e414011a8aa320/fdce9c2b4a52e0c7?lnk=gst&q=xdat_element_access#fdce9c2b4a52e0c7

I would recommend the following steps:

· Backup the database using pg_dump

· Run this SQL in the above post

· In the webapp go to Administration -> More Options -> Clear DB Cache

· Logout and log back in… maybe even restart tomcat just to make sure all caching is purged.

There could be something else wrong to, but this was the first obvious thing I found.

Alex

unread,

Mar 25, 2011, 12:27:45 AM3/25/11

to xnat_discussion

Tim,

I followed the directions from the referenced thread, cleared DB cache
and restarted tomcat. I don't see any improvements. What else do you
think could be wrong?

Thanks, Alex.

On Mar 9, 1:26 pm, "Olsen, Tim" <ols...@mir.wustl.edu> wrote:
> It looks like this project was created on a 1.4 RC version which had a permissions bug. Unfortunately, I think the clearest way to fix it is to do some light surgery on your database.
>
> I detail the SQL that should be run here:
>

> http://groups.google.com/group/xnat_discussion/browse_thread/thread/3...

>
> I would recommend the following steps:
>

> * Backup the database using pg_dump
>
> * Run this SQL in the above post
>
> * In the webapp go to Administration -> More Options -> Clear DB Cache
>
> * Logout and log back in... maybe even restart tomcat just to make sure all caching is purged.

>
> There could be something else wrong to, but this was the first obvious thing I found.
>
> Tim
>
>
>
>
>
>
>
> -----Original Message-----
> From: xnat_di...@googlegroups.com [mailto:xnat_di...@googlegroups.com] On Behalf Of Alex
> Sent: Thursday, March 03, 2011 1:53 PM
> To: xnat_discussion
> Subject: Re: Possible 1.4.2 bugs
>
> I can see the affected project's experiments in the list.
>

> On Mar 3, 2:19 pm, "Olsen, Tim" <ols...@mir.wustl.edu<mailto:ols...@mir.wustl.edu>> wrote:
>
> > Do the experiments for the affected project show up? If you do that URL as an admin account, you should see all experiments in your database.
>
> > Tim
>
> > -----Original Message-----
>
> > From: xnat_di...@googlegroups.com
>
> > [mailto:xnat_di...@googlegroups.com] On Behalf Of Alex
>
> > Sent: Thursday, March 03, 2011 1:06 PM
>
> > To: xnat_discussion
>
> > Subject: Re: Possible 1.4.2 bugs
>
> > That gives me a list of experiment ids, project ids, date, xsiType, label, insert date and URI.
>

> > On Mar 3, 1:24 pm, "Olsen, Tim" <ols...@mir.wustl.edu<mailto:ols...@mir.wustl.edu>> wrote:
>
> > > Ah. That's broken too. How about if you go to HOST/REST/experiments?format=html ?
>
> > > -----Original Message-----
>
> > > From: xnat_di...@googlegroups.com
>
> > > [mailto:xnat_di...@googlegroups.com] On Behalf Of Alex
>
> > > Sent: Thursday, March 03, 2011 12:23 PM
>
> > > To: xnat_discussion
>
> > > Subject: Re: Possible 1.4.2 bugs
>
> > > Data doesn't expand and when I click on Data nothing happens, no javascript errors either.
>
> > > Alex.
>

> > > On Mar 3, 10:58 am, "Olsen, Tim" <ols...@mir.wustl.edu<mailto:ols...@mir.wustl.edu>> wrote:
>
> > > > To go back a few emails, can you see the subjects or sessions when you view ALL using the data link on the left.
>
> > > > > When you view all subjects, (via the left bar -> Data -> Subjects) do subjects for this project show up?
>
> > > > Tim
>
> > > > -----Original Message-----
>
> > > > From: xnat_di...@googlegroups.com
>
> > > > [mailto:xnat_di...@googlegroups.com] On Behalf Of Alex
>
> > > > Sent: Wednesday, March 02, 2011 4:34 PM
>
> > > > To: xnat_discussion
>
> > > > Subject: Re: Possible 1.4.2 bugs
>
> > > > I do not see any javascript errors or server errors in Chrome's Developer Tools.
>
> > > > Here's a capture of XHR for a project that doesn't
>
> > > > work:http://goo.gl/iWlov
>
> > > > Here's one for a project that works:http://goo.gl/wjB0d
>
> > > > Alex.
>

> > > > On Mar 2, 12:42 am, Tim Olsen <ols...@mir.wustl.edu<mailto:ols...@mir.wustl.edu>> wrote:
>
> > > > > The problem we had locally involved project IDs that started
>
> > > > > with integers. Sounds like a different issue, though with similar effect.
>
> > > > > There tends to be some log4j confusion when two XNATs are
>
> > > > > running on the same server. We generally can avoid running two
>
> > > > > XNATs on the same machine, so its been a low priority bug.
>
> > > > > Are there any javascript errors on the page? The bottom tabs
>
> > > > > are loaded via AJAX, if you view the Network or Resource traffic
>
> > > > > in Firefox -> Firebug or Chrome -> Developer Tools does it
>
> > > > > notify you of any issues? Any server calls returning a 500 status code?
>
> > > > > Tim
>

> > > > > On Mar 1, 10:49 pm, Alex <skiz...@gmail.com<mailto:skiz...@gmail.com>> wrote:
>
> > > > > > The ID is "TP" (without quotes). Project title has an opening
>
> > > > > > and a closing parenthesis: "Test (Alex)" (without quotes). I
>
> > > > > > tried changing title to remove the parenthesis - that didn't help.
>
> > > > > > I'm running this instance (1.4.2) of XNAT in parallel to our
>
> > > > > > production XNAT. I noticed that the the logs in webapps/
>
> > > > > > <1.4.2_project_name>/logs are not updated for some reason. The
>
> > > > > > logs in the production XNAT are updated. I guess that's why I
>
> > > > > > don't see any errors in the logs. What could be the reason for that?
>
> > > > > > Alex.
>

> > > > > > On Mar 1, 5:22 pm, "Olsen, Tim" <ols...@mir.wustl.edu<mailto:ols...@mir.wustl.edu>> wrote:
>
> > > > > > > Regarding the problematic project page, does the project ID for this project include any odd characters? What is the Project ID? We've had a similar bug on one of our servers.
>
> > > > > > > Tim
>
> > > > > > > -----Original Message-----
>
> > > > > > > From: xnat_di...@googlegroups.com
>
> > > > > > > [mailto:xnat_di...@googlegroups.com] On Behalf Of Alex
>
> > > > > > > Sent: Wednesday, February 16, 2011 7:11 PM
>
> > > > > > > To: xnat_discussion
>
> > > > > > > Subject: Re: Possible 1.4.2 bugs
>
> > > > > > > Sorry for bumping this, but are there any more suggestions about these issues in 1.4.2?
>

> > > > > > > On Feb 3, 9:07 pm, Alex <skiz...@gmail.com<mailto:skiz...@gmail.com>> wrote:
>
> > > > > > > > I'm testing 1.4.2 that was upgraded from 1.4rc3 with a
>
> > > > > > > > copy of the original database. I came across a few
>
> > > > > > > > problems that might be bugs, please see below for description and screen captures.
>
> > > > > > > > 1. When I go to unassigned prearchive and click on a study
>
> > > > > > > > link, it takes me to session detail. Instead of project
>
> > > > > > > > name combo box, it
>
> > > > > > > > shows: $om.getProject($project,false).getDisplayID()https://docs.google.com/leaf?id=0B5EqZ7UllzwSNDRlZTZkNTYtY2ZkYy00N2E3...
>
> > > > > > > > 2. When I go to Advanced Search, the Select Pivot
>
> > > > > > > > Data-type to search combo box is empty.https://docs.google.com/leaf?id=0B5EqZ7UllzwSN2YxNTI1OWItYzhlZC00ODI0...
>
> > > > > > > > 3. When I pick one of the projects off the main page, it
>
> > > > > > > > displays just the top tab panel (Details, Access...), but
>
> > > > > > > > not the lower tab panel (Subjects and so on). That happens only in one of the projects.https://docs.google.com/leaf?id=0B5EqZ7UllzwSYzZlN2E1ZDItZWM2NS00ZDlm...
>
> > > > > > > > Any ideas on how to fix these?
>
> > > > > > > > Thanks, Alex.
>
> > > > > > > --
>
> > > > > > > You received this message because you are subscribed to the Google Groups "xnat_discussion" group.
>

> > > > > > > To post to this group, send email to xnat_di...@googlegroups.com<mailto:xnat_di...@googlegroups.com>.
>
> > > > > > > To unsubscribe from this group, send email to xnat_discussi...@googlegroups.com<mailto:xnat_discussion+unsubsc ri...@googlegroups.com>.

>
> > > > > > > For more options, visit this group athttp://groups.google.com/group/xnat_discussion?hl=en.
>
> > > > > > > The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
>
> > > > --
>
> > > > You received this message because you are subscribed to the Google Groups "xnat_discussion" group.
>

> > > > To post to this group, send email to xnat_di...@googlegroups.com<mailto:xnat_di...@googlegroups.com>.
>
> > > > To unsubscribe from this group, send email to xnat_discussi...@googlegroups.com<mailto:xnat_discussion+unsubsc ri...@googlegroups.com>.

>
> > > > For more options, visit this group athttp://groups.google.com/group/xnat_discussion?hl=en.
>
> > > > The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
>
> > > --
>
> > > You received this message because you are subscribed to the Google Groups "xnat_discussion" group.
>

> > > To post to this group, send email to xnat_di...@googlegroups.com<mailto:xnat_di...@googlegroups.com>.
>
> > > To unsubscribe from this group, send email to xnat_discussi...@googlegroups.com<mailto:xnat_discussion+unsubsc ri...@googlegroups.com>.

>
> > > For more options, visit this group athttp://groups.google.com/group/xnat_discussion?hl=en.
>
> > > The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
>
> > --
>
> > You received this message because you are subscribed to the Google Groups "xnat_discussion" group.
>

> > To post to this group, send email to xnat_di...@googlegroups.com<mailto:xnat_di...@googlegroups.com>.
>
> > To unsubscribe from this group, send email to xnat_discussi...@googlegroups.com<mailto:xnat_discussion+unsubsc ri...@googlegroups.com>.

>
> > For more options, visit this group athttp://groups.google.com/group/xnat_discussion?hl=en.
>
> > The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action
>

> ...
>
> read more »

Alex

unread,

Mar 27, 2011, 9:51:36 PM3/27/11

to xnat_discussion

Tim,

I tried to upgrade to 1.5rc1 - got exactly the same symptoms as in
1.4.2. The good news is that I was able to get the logs working in
1.5rc1. Below is the output from the log files from 1.5rc1 upgrade.
Please let me know if that information will clarify the source of the
problem.

Thanks, Alex.

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

Logs output on login:

xdat.log:

2011-03-27 20:32:04,517 [main] ERROR
org.nrg.xnat.restlet.servlet.XNATRestletServlet - error starting DICOM
SCP
java.net.BindException: Permission denied
at java.net.PlainSocketImpl.socketBind(Native Method)
at java.net.PlainSocketImpl.bind(PlainSocketImpl.java:359)
at java.net.ServerSocket.bind(ServerSocket.java:319)
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:104)
at
org.nrg.xnat.restlet.servlet.XNATRestletServlet.startDicomSCP(XNATRestletServlet.java:
68)
at
org.nrg.xnat.restlet.servlet.XNATRestletServlet.init(XNATRestletServlet.java:
42)
at javax.servlet.GenericServlet.init(GenericServlet.java:212)
at
org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:
1139)
at
org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:
966)
at
org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:
3956)
at
org.apache.catalina.core.StandardContext.start(StandardContext.java:
4230)
at
org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:
760)
at
org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:
740)
at
org.apache.catalina.core.StandardHost.addChild(StandardHost.java:544)
at
org.apache.catalina.startup.HostConfig.deployDirectory(HostConfig.java:
927)
at
org.apache.catalina.startup.HostConfig.deployDirectories(HostConfig.java:
890)
at
org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:492)
at
org.apache.catalina.startup.HostConfig.start(HostConfig.java:1150)
at
org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:
311)
at
org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:
120)
at
org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1022)
at
org.apache.catalina.core.StandardHost.start(StandardHost.java:736)
at
org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1014)
at
org.apache.catalina.core.StandardEngine.start(StandardEngine.java:443)
at
org.apache.catalina.core.StandardService.start(StandardService.java:
448)
at
org.apache.catalina.core.StandardServer.start(StandardServer.java:700)
at org.apache.catalina.startup.Catalina.start(Catalina.java:
552)
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:
295)
at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:
433)
2011-03-27 20:32:15,992 [http-8080-Processor21] ERROR
org.nrg.xdat.security.XDATUser -
org.nrg.xft.exception.ElementNotFoundException: Element not found:
'fs:automaticSegmentationData'
at
org.nrg.xft.meta.XFTMetaManager.FindElement(XFTMetaManager.java:224)
at
org.nrg.xft.meta.XFTMetaManager.GetWrappedElementByName(XFTMetaManager.java:
368)
at
org.nrg.xft.schema.Wrappers.GenericWrapper.GenericWrapperElement.GetElement(GenericWrapperElement.java:
167)
at
org.nrg.xdat.schema.SchemaElement.GetElement(SchemaElement.java:112)
at
org.nrg.xdat.security.ElementSecurity.getSchemaElement(ElementSecurity.java:
495)
at
org.nrg.xdat.security.XDATUser.getUnSecuredElements(XDATUser.java:843)
at
org.nrg.xdat.security.XDATUser.getReadableElementDisplays(XDATUser.java:
695)
at
org.nrg.xdat.security.XDATUser.getBrowseableElementDisplays(XDATUser.java:
1613)
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.velocity.runtime.parser.node.ASTMethod.execute(ASTMethod.java:
260)
at
org.apache.velocity.runtime.parser.node.ASTReference.execute(ASTReference.java:
207)
at
org.apache.velocity.runtime.parser.node.ASTReference.value(ASTReference.java:
357)
at
org.apache.velocity.runtime.parser.node.ASTSetDirective.render(ASTSetDirective.java:
135)
at
org.apache.velocity.runtime.parser.node.ASTBlock.render(ASTBlock.java:
94)
at
org.apache.velocity.runtime.parser.node.ASTIfStatement.render(ASTIfStatement.java:
109)
at
org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.java:
271)
at org.apache.velocity.Template.merge(Template.java:296)
at
org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:492)
at
org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:461)
at
org.apache.turbine.services.velocity.TurbineVelocityService.executeRequest(TurbineVelocityService.java:
415)
at
org.apache.turbine.services.velocity.TurbineVelocityService.handleRequest(TurbineVelocityService.java:
281)
at
org.apache.turbine.services.velocity.TurbineVelocity.handleRequest(TurbineVelocity.java:
71)
at
org.apache.turbine.modules.navigations.VelocityNavigation.buildTemplate(VelocityNavigation.java:
100)
at
org.apache.turbine.modules.navigations.TemplateNavigation.doBuild(TemplateNavigation.java:
66)
at org.apache.turbine.modules.Navigation.build(Navigation.java:
57)
at
org.apache.turbine.modules.NavigationLoader.eval(NavigationLoader.java:
104)
at
org.apache.turbine.util.template.TemplateNavigation.toString(TemplateNavigation.java:
106)
at
org.apache.velocity.runtime.parser.node.ASTReference.render(ASTReference.java:
321)
at
org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.java:
271)
at org.apache.velocity.Template.merge(Template.java:296)
at
org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:492)
at
org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:461)
at
org.apache.turbine.services.velocity.TurbineVelocityService.executeRequest(TurbineVelocityService.java:
415)
at
org.apache.turbine.services.velocity.TurbineVelocityService.handleRequest(TurbineVelocityService.java:
281)
at
org.apache.turbine.services.velocity.TurbineVelocity.handleRequest(TurbineVelocity.java:
71)
at
org.apache.turbine.modules.layouts.VelocityOnlyLayout.doBuild(VelocityOnlyLayout.java:
116)
at org.apache.turbine.modules.Layout.build(Layout.java:53)
at
org.apache.turbine.modules.LayoutLoader.exec(LayoutLoader.java:98)
at
org.apache.turbine.modules.pages.DefaultPage.doBuild(DefaultPage.java:
146)
at org.apache.turbine.modules.Page.build(Page.java:53)
at org.apache.turbine.modules.PageLoader.exec(PageLoader.java:
98)
at org.apache.turbine.Turbine.doGet(Turbine.java:751)
at org.apache.turbine.Turbine.doPost(Turbine.java:846)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:
647)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:
729)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:
269)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:
188)
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:
213)
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:
172)
at
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:
433)
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:
127)
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:
117)
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:
108)
at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:
174)
at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:
875)
at org.apache.coyote.http11.Http11BaseProtocol
$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:
665)
at
org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:
528)
at
org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:
81)
at org.apache.tomcat.util.threads.ThreadPool
$ControlRunnable.run(ThreadPool.java:689)
at java.lang.Thread.run(Thread.java:619)

velocity.log:

2011-03-27 20:32:02,812 [main] ERROR velocity - VM #xdatSearchForm:
error : too few arguments to macro. Wanted 2 got 0
2011-03-27 20:32:02,838 [main] ERROR velocity - VM #displayFileSystem:
error : too few arguments to macro. Wanted 1 got 0
2011-03-27 20:32:05,086 [http-8080-Processor24] ERROR velocity - Left
side ($data.getSession().getAttribute("user").getUserna
me()) of '==' operation has null value. If a reference, it may not be
in the context. Operation not possible. navigations//No
MenuTop.vm [line 9, column 76]
2011-03-27 20:32:05,087 [http-8080-Processor25] ERROR velocity - Left
side ($data.getSession().getAttribute("user").getUserna
me()) of '==' operation has null value. If a reference, it may not be
in the context. Operation not possible. navigations//No
MenuTop.vm [line 9, column 76]

axis.log:

10812 [main] ERROR
org.apache.axis.configuration.EngineConfigurationFactoryServlet -
Unable to find config file. Creating n
ew servlet engine config file: /WEB-INF/server-config.wsdd

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

Logs output on defective project access:

turbine.log:

2011-03-27 20:35:59,622 [http-8080-Processor19] ERROR
org.apache.turbine.services.velocity.TurbineVelocityService - Class
jav
a.util.ArrayList.get threw Exception
java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
at java.util.ArrayList.RangeCheck(ArrayList.java:547)
at java.util.ArrayList.get(ArrayList.java:322)
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.velocity.runtime.parser.node.ASTMethod.execute(ASTMethod.java:
260)
at
org.apache.velocity.runtime.parser.node.ASTReference.execute(ASTReference.java:
207)
at
org.apache.velocity.runtime.parser.node.ASTReference.value(ASTReference.java:
357)
at
org.apache.velocity.runtime.parser.node.ASTSetDirective.render(ASTSetDirective.java:
135)
at
org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.java:
271)
at org.apache.velocity.Template.merge(Template.java:296)
at
org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:492)
at
org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:461)
at
org.apache.turbine.services.velocity.TurbineVelocityService.executeRequest(TurbineVelocityService.java:
415)
at
org.apache.turbine.services.velocity.TurbineVelocityService.handleRequest(TurbineVelocityService.java:
281)
at
org.apache.turbine.services.velocity.TurbineVelocity.handleRequest(TurbineVelocity.java:
71)
at
org.apache.turbine.modules.screens.VelocityScreen.buildTemplate(VelocityScreen.java:
119)
at
org.apache.turbine.modules.screens.TemplateScreen.doBuild(TemplateScreen.java:
101)
at org.apache.turbine.modules.Screen.build(Screen.java:57)
at
org.apache.turbine.modules.ScreenLoader.eval(ScreenLoader.java:104)
at
org.apache.turbine.modules.layouts.VelocityOnlyLayout.doBuild(VelocityOnlyLayout.java:
92)
at org.apache.turbine.modules.Layout.build(Layout.java:53)
at
org.apache.turbine.modules.LayoutLoader.exec(LayoutLoader.java:98)
at
org.apache.turbine.modules.pages.DefaultPage.doBuild(DefaultPage.java:
146)
at org.apache.turbine.modules.Page.build(Page.java:53)
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:
627)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:
729)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:
269)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:
188)
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:
213)
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:
172)
at
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:
433)
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:
127)
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:
117)
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:
108)
at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:
174)
at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:
875)
at org.apache.coyote.http11.Http11BaseProtocol
$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:
665)
at
org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:
528)
at
org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:
81)
at org.apache.tomcat.util.threads.ThreadPool
$ControlRunnable.run(ThreadPool.java:689)
at java.lang.Thread.run(Thread.java:619)
2011-03-27 20:35:59,735 [http-8080-Processor19] ERROR
org.apache.turbine.services.velocity.TurbineVelocityService - Class
org
.nrg.xdat.om.XnatProjectdata.getBundles threw Exception
java.lang.NullPointerException
at
org.nrg.xdat.om.base.BaseXnatProjectdata.getBundles(BaseXnatProjectdata.java:
1160)
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.velocity.runtime.parser.node.ASTMethod.execute(ASTMethod.java:
260)
at
org.apache.velocity.runtime.parser.node.ASTReference.execute(ASTReference.java:
207)
at
org.apache.velocity.runtime.parser.node.ASTReference.value(ASTReference.java:
357)
at
org.apache.velocity.runtime.parser.node.ASTSetDirective.render(ASTSetDirective.java:
135)
at
org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.java:
271)
at
org.apache.velocity.runtime.directive.Parse.render(Parse.java:232)
at
org.apache.velocity.runtime.parser.node.ASTDirective.render(ASTDirective.java:
153)
at
org.apache.velocity.runtime.parser.node.ASTBlock.render(ASTBlock.java:
94)
at
org.apache.velocity.runtime.parser.node.ASTIfStatement.render(ASTIfStatement.java:
109)
at
org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.java:
271)
at org.apache.velocity.Template.merge(Template.java:296)
at
org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:492)
at
org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:461)
at
org.apache.turbine.services.velocity.TurbineVelocityService.executeRequest(TurbineVelocityService.java:
415)
at
org.apache.turbine.services.velocity.TurbineVelocityService.handleRequest(TurbineVelocityService.java:
281)
at
org.apache.turbine.services.velocity.TurbineVelocity.handleRequest(TurbineVelocity.java:
71)
at
org.apache.turbine.modules.screens.VelocityScreen.buildTemplate(VelocityScreen.java:
119)
at
org.apache.turbine.modules.screens.TemplateScreen.doBuild(TemplateScreen.java:
101)
at org.apache.turbine.modules.Screen.build(Screen.java:57)
at
org.apache.turbine.modules.ScreenLoader.eval(ScreenLoader.java:104)
at
org.apache.turbine.modules.layouts.VelocityOnlyLayout.doBuild(VelocityOnlyLayout.java:
92)
at org.apache.turbine.modules.Layout.build(Layout.java:53)
at
org.apache.turbine.modules.LayoutLoader.exec(LayoutLoader.java:98)
at
org.apache.turbine.modules.pages.DefaultPage.doBuild(DefaultPage.java:
146)
at org.apache.turbine.modules.Page.build(Page.java:53)
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:
627)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:
729)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:
269)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:
188)
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:
213)
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:
172)
at
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:
433)
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:
127)
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:
117)
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:
108)
at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:
174)
at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:
875)
at org.apache.coyote.http11.Http11BaseProtocol
$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:
665)
at
org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:
528)
at
org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:
81)
at org.apache.tomcat.util.threads.ThreadPool
$ControlRunnable.run(ThreadPool.java:689)
at java.lang.Thread.run(Thread.java:619)

velocity.log:

2011-03-27 20:35:59,707 [http-8080-Processor19] ERROR velocity - RHS
of #set statement is null. Context will not be modified.
/screens/xnat_projectData/xnat_projectData_actions_box.vm [line 21,
column 1]
2011-03-27 20:35:59,708 [http-8080-Processor19] ERROR velocity - RHS
of #set statement is null. Context will not be modified.
/screens/xnat_projectData/xnat_projectData_actions_box.vm [line 21,
column 1]
2011-03-27 20:35:59,708 [http-8080-Processor19] ERROR velocity - RHS
of #set statement is null. Context will not be modified.
/screens/xnat_projectData/xnat_projectData_actions_box.vm [line 21,
column 1]
2011-03-27 20:35:59,708 [http-8080-Processor19] ERROR velocity - RHS
of #set statement is null. Context will not be modified.
/screens/xnat_projectData/xnat_projectData_actions_box.vm [line 21,
column 1]
2011-03-27 20:35:59,735 [http-8080-Processor19] ERROR velocity - Left
side ($bundles.size()) of '>' operation has null value.
Operation not possible. /screens/xnat_projectData/
xnat_projectData_bundle_tabs.vm [line 2, column 34]
2011-03-27 20:35:59,796 [http-8080-Processor19] ERROR velocity - Left
side ($om.getItem().getGenericSchemaElement().getPrimar
yElements().indexOf("xnat:experimentData")) of '!=' operation has null
value. Operation not possible. navigations//Breadcrumb
.vm [line 127, column 108

xdat.log:

2011-03-27 20:35:59,727 [http-8080-Processor19] ERROR
org.nrg.xdat.om.base.auto.AutoXnatProjectdata -
org.nrg.xft.exception.ElementNotFoundException: Element not found:
'fs:asegRegionAnalysis'
at
org.nrg.xft.meta.XFTMetaManager.FindElement(XFTMetaManager.java:224)
at
org.nrg.xft.meta.XFTMetaManager.GetWrappedElementByName(XFTMetaManager.java:
368)
at
org.nrg.xft.schema.Wrappers.GenericWrapper.GenericWrapperElement.GetElement(GenericWrapperElement.java:
167)
at
org.nrg.xdat.om.base.BaseXnatProjectdata.getDefaultSearch(BaseXnatProjectdata.java:
1246)
at
org.nrg.xdat.om.base.BaseXnatProjectdata.getBundles(BaseXnatProjectdata.java:
1137)
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.velocity.runtime.parser.node.ASTMethod.execute(ASTMethod.java:
260)
at
org.apache.velocity.runtime.parser.node.ASTReference.execute(ASTReference.java:
207)
at
org.apache.velocity.runtime.parser.node.ASTReference.value(ASTReference.java:
357)
at
org.apache.velocity.runtime.parser.node.ASTSetDirective.render(ASTSetDirective.java:
135)
at
org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.java:
271)
at
org.apache.velocity.runtime.directive.Parse.render(Parse.java:232)
at
org.apache.velocity.runtime.parser.node.ASTDirective.render(ASTDirective.java:
153)
at
org.apache.velocity.runtime.parser.node.ASTBlock.render(ASTBlock.java:
94)
at
org.apache.velocity.runtime.parser.node.ASTIfStatement.render(ASTIfStatement.java:
109)
at
org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.java:
271)
at org.apache.velocity.Template.merge(Template.java:296)
at
org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:492)
at
org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:461)
at
org.apache.turbine.services.velocity.TurbineVelocityService.executeRequest(TurbineVelocityService.java:
415)
at
org.apache.turbine.services.velocity.TurbineVelocityService.handleRequest(TurbineVelocityService.java:
281)
at
org.apache.turbine.services.velocity.TurbineVelocity.handleRequest(TurbineVelocity.java:
71)
at
org.apache.turbine.modules.screens.VelocityScreen.buildTemplate(VelocityScreen.java:
119)
at
org.apache.turbine.modules.screens.TemplateScreen.doBuild(TemplateScreen.java:
101)
at org.apache.turbine.modules.Screen.build(Screen.java:57)
at
org.apache.turbine.modules.ScreenLoader.eval(ScreenLoader.java:104)
at
org.apache.turbine.modules.layouts.VelocityOnlyLayout.doBuild(VelocityOnlyLayout.java:
92)
at org.apache.turbine.modules.Layout.build(Layout.java:53)
at
org.apache.turbine.modules.LayoutLoader.exec(LayoutLoader.java:98)
at
org.apache.turbine.modules.pages.DefaultPage.doBuild(DefaultPage.java:
146)
at org.apache.turbine.modules.Page.build(Page.java:53)
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:
627)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:
729)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:
269)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:
188)
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:
213)
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:
172)
at
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:
433)
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:
127)
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:
117)
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:
108)
at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:
174)
at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:
875)
at org.apache.coyote.http11.Http11BaseProtocol
$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:
665)
at
org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:
528)
at
org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:
81)
at org.apache.tomcat.util.threads.ThreadPool
$ControlRunnable.run(ThreadPool.java:689)
at java.lang.Thread.run(Thread.java:619)
2011-03-27 20:35:59,733 [http-8080-Processor19] ERROR
org.nrg.xdat.om.base.auto.AutoXnatProjectdata -
org.nrg.xft.exception.ElementNotFoundException: Element not found:
'fs:aparcRegionAnalysis'
at
org.nrg.xft.meta.XFTMetaManager.FindElement(XFTMetaManager.java:224)
at
org.nrg.xft.meta.XFTMetaManager.GetWrappedElementByName(XFTMetaManager.java:
368)
at
org.nrg.xft.schema.Wrappers.GenericWrapper.GenericWrapperElement.GetElement(GenericWrapperElement.java:
167)
at
org.nrg.xdat.om.base.BaseXnatProjectdata.getDefaultSearch(BaseXnatProjectdata.java:
1246)
at
org.nrg.xdat.om.base.BaseXnatProjectdata.getBundles(BaseXnatProjectdata.java:
1137)
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.velocity.runtime.parser.node.ASTMethod.execute(ASTMethod.java:
260)
at
org.apache.velocity.runtime.parser.node.ASTReference.execute(ASTReference.java:
207)
at
org.apache.velocity.runtime.parser.node.ASTReference.value(ASTReference.java:
357)
at
org.apache.velocity.runtime.parser.node.ASTSetDirective.render(ASTSetDirective.java:
135)
at
org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.java:
271)
at
org.apache.velocity.runtime.directive.Parse.render(Parse.java:232)
at
org.apache.velocity.runtime.parser.node.ASTDirective.render(ASTDirective.java:
153)
at
org.apache.velocity.runtime.parser.node.ASTBlock.render(ASTBlock.java:
94)
at
org.apache.velocity.runtime.parser.node.ASTIfStatement.render(ASTIfStatement.java:
109)
at
org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.java:
271)
at org.apache.velocity.Template.merge(Template.java:296)
at
org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:492)
at
org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:461)
at
org.apache.turbine.services.velocity.TurbineVelocityService.executeRequest(TurbineVelocityService.java:
415)
at
org.apache.turbine.services.velocity.TurbineVelocityService.handleRequest(TurbineVelocityService.java:
281)
at
org.apache.turbine.services.velocity.TurbineVelocity.handleRequest(TurbineVelocity.java:
71)
at
org.apache.turbine.modules.screens.VelocityScreen.buildTemplate(VelocityScreen.java:
119)
at
org.apache.turbine.modules.screens.TemplateScreen.doBuild(TemplateScreen.java:
101)
at org.apache.turbine.modules.Screen.build(Screen.java:57)
at
org.apache.turbine.modules.ScreenLoader.eval(ScreenLoader.java:104)
at
org.apache.turbine.modules.layouts.VelocityOnlyLayout.doBuild(VelocityOnlyLayout.java:
92)
at org.apache.turbine.modules.Layout.build(Layout.java:53)
at
org.apache.turbine.modules.LayoutLoader.exec(LayoutLoader.java:98)
at
org.apache.turbine.modules.pages.DefaultPage.doBuild(DefaultPage.java:
146)
at org.apache.turbine.modules.Page.build(Page.java:53)
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:
627)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:
729)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:
269)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:
188)
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:
213)
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:
172)
at
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:
433)
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:
127)
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:
117)
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:
108)
at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:
174)
at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:
875)
at org.apache.coyote.http11.Http11BaseProtocol
$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:
665)
at
org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:
528)
at
org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:
81)
at org.apache.tomcat.util.threads.ThreadPool
$ControlRunnable.run(ThreadPool.java:689)
at java.lang.Thread.run(Thread.java:619)
2011-03-27 20:35:59,734 [http-8080-Processor19] ERROR
org.nrg.xdat.om.base.auto.AutoXnatProjectdata -
org.nrg.xft.exception.ElementNotFoundException: Element not found:
'fs:asegRegionAnalysis'
at
org.nrg.xft.meta.XFTMetaManager.FindElement(XFTMetaManager.java:224)
at
org.nrg.xft.meta.XFTMetaManager.GetWrappedElementByName(XFTMetaManager.java:
368)
at
org.nrg.xft.schema.Wrappers.GenericWrapper.GenericWrapperElement.GetElement(GenericWrapperElement.java:
167)
at
org.nrg.xdat.schema.SchemaElement.GetElement(SchemaElement.java:112)
at
org.nrg.xdat.search.DisplaySearch.setRootElement(DisplaySearch.java:
1333)
at
org.nrg.xdat.om.base.BaseXnatProjectdata.getDefaultSearch(BaseXnatProjectdata.java:
1690)
at
org.nrg.xdat.om.base.BaseXnatProjectdata.getDefaultSearch(BaseXnatProjectdata.java:
1173)
at
org.nrg.xdat.om.base.BaseXnatProjectdata.getBundles(BaseXnatProjectdata.java:
1158)
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.velocity.runtime.parser.node.ASTMethod.execute(ASTMethod.java:
260)
at
org.apache.velocity.runtime.parser.node.ASTReference.execute(ASTReference.java:
207)
at
org.apache.velocity.runtime.parser.node.ASTReference.value(ASTReference.java:
357)
at
org.apache.velocity.runtime.parser.node.ASTSetDirective.render(ASTSetDirective.java:
135)
at
org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.java:
271)
at
org.apache.velocity.runtime.directive.Parse.render(Parse.java:232)
at
org.apache.velocity.runtime.parser.node.ASTDirective.render(ASTDirective.java:
153)
at
org.apache.velocity.runtime.parser.node.ASTBlock.render(ASTBlock.java:
94)
at
org.apache.velocity.runtime.parser.node.ASTIfStatement.render(ASTIfStatement.java:
109)
at
org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.java:
271)
at org.apache.velocity.Template.merge(Template.java:296)
at
org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:492)
at
org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:461)
at
org.apache.turbine.services.velocity.TurbineVelocityService.executeRequest(TurbineVelocityService.java:
415)
at
org.apache.turbine.services.velocity.TurbineVelocityService.handleRequest(TurbineVelocityService.java:
281)
at
org.apache.turbine.services.velocity.TurbineVelocity.handleRequest(TurbineVelocity.java:
71)
at
org.apache.turbine.modules.screens.VelocityScreen.buildTemplate(VelocityScreen.java:
119)
at
org.apache.turbine.modules.screens.TemplateScreen.doBuild(TemplateScreen.java:
101)
at org.apache.turbine.modules.Screen.build(Screen.java:57)
at
org.apache.turbine.modules.ScreenLoader.eval(ScreenLoader.java:104)
at
org.apache.turbine.modules.layouts.VelocityOnlyLayout.doBuild(VelocityOnlyLayout.java:
92)
at org.apache.turbine.modules.Layout.build(Layout.java:53)
at
org.apache.turbine.modules.LayoutLoader.exec(LayoutLoader.java:98)
at
org.apache.turbine.modules.pages.DefaultPage.doBuild(DefaultPage.java:
146)
at org.apache.turbine.modules.Page.build(Page.java:53)
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:
627)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:
729)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:
269)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:
188)
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:
213)
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:
172)
at
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:
433)
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:
127)
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:
117)
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:
108)
at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:
174)
at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:
875)
at org.apache.coyote.http11.Http11BaseProtocol
$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:
665)
at
org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:
528)
at
org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:
81)
at org.apache.tomcat.util.threads.ThreadPool
$ControlRunnable.run(ThreadPool.java:689)
at java.lang.Thread.run(Thread.java:619)
2011-03-27 20:35:59,734 [http-8080-Processor19] ERROR
org.nrg.xdat.om.base.auto.AutoXnatProjectdata -
java.lang.NullPointerException
at
org.nrg.xdat.om.base.BaseXnatProjectdata.getDefaultSearch(BaseXnatProjectdata.java:
1175)
at
org.nrg.xdat.om.base.BaseXnatProjectdata.getBundles(BaseXnatProjectdata.java:
1158)
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.velocity.runtime.parser.node.ASTMethod.execute(ASTMethod.java:
260)
at
org.apache.velocity.runtime.parser.node.ASTReference.execute(ASTReference.java:
207)
at
org.apache.velocity.runtime.parser.node.ASTReference.value(ASTReference.java:
357)
at
org.apache.velocity.runtime.parser.node.ASTSetDirective.render(ASTSetDirective.java:
135)
at
org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.java:
271)
at
org.apache.velocity.runtime.directive.Parse.render(Parse.java:232)
at
org.apache.velocity.runtime.parser.node.ASTDirective.render(ASTDirective.java:
153)
at
org.apache.velocity.runtime.parser.node.ASTBlock.render(ASTBlock.java:
94)
at
org.apache.velocity.runtime.parser.node.ASTIfStatement.render(ASTIfStatement.java:
109)
at
org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.java:
271)
at org.apache.velocity.Template.merge(Template.java:296)
at
org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:492)
at
org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:461)
at
org.apache.turbine.services.velocity.TurbineVelocityService.executeRequest(TurbineVelocityService.java:
415)
at
org.apache.turbine.services.velocity.TurbineVelocityService.handleRequest(TurbineVelocityService.java:
281)
at
org.apache.turbine.services.velocity.TurbineVelocity.handleRequest(TurbineVelocity.java:
71)
at
org.apache.turbine.modules.screens.VelocityScreen.buildTemplate(VelocityScreen.java:
119)
at
org.apache.turbine.modules.screens.TemplateScreen.doBuild(TemplateScreen.java:
101)
at org.apache.turbine.modules.Screen.build(Screen.java:57)
at
org.apache.turbine.modules.ScreenLoader.eval(ScreenLoader.java:104)
at
org.apache.turbine.modules.layouts.VelocityOnlyLayout.doBuild(VelocityOnlyLayout.java:
92)
at org.apache.turbine.modules.Layout.build(Layout.java:53)
at
org.apache.turbine.modules.LayoutLoader.exec(LayoutLoader.java:98)
at
org.apache.turbine.modules.pages.DefaultPage.doBuild(DefaultPage.java:
146)
at org.apache.turbine.modules.Page.build(Page.java:53)
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:
627)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:
729)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:
269)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:
188)
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:
213)
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:
172)
at
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:
433)
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:
127)
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:
117)
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:
108)
at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:
174)
at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:
875)
at org.apache.coyote.http11.Http11BaseProtocol
$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:
665)
at
org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:
528)
at
org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:
81)
at org.apache.tomcat.util.threads.ThreadPool
$ControlRunnable.run(ThreadPool.java:689)
at java.lang.Thread.run(Thread.java:619)

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

Logs output on going to advanced search:

xdat.log:

2011-03-27 20:45:34,992 [http-8080-Processor22] ERROR
org.nrg.xdat.security.XDATUser -
org.nrg.xft.exception.ElementNotFoundException: Element not found:
'fs:automaticSegmentationData'
at
org.nrg.xft.meta.XFTMetaManager.FindElement(XFTMetaManager.java:224)
at
org.nrg.xft.meta.XFTMetaManager.GetWrappedElementByName(XFTMetaManager.java:
368)
at
org.nrg.xft.schema.Wrappers.GenericWrapper.GenericWrapperElement.GetElement(GenericWrapperElement.java:
167)
at
org.nrg.xdat.schema.SchemaElement.GetElement(SchemaElement.java:112)
at
org.nrg.xdat.security.ElementSecurity.getSchemaElement(ElementSecurity.java:
495)
at
org.nrg.xdat.security.XDATUser.getUnSecuredElements(XDATUser.java:843)
at
org.nrg.xdat.security.XDATUser.getReadableElementDisplays(XDATUser.java:
695)
at
org.nrg.xdat.security.XDATUser.getSearchableElementDisplays(XDATUser.java:
1680)
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.velocity.runtime.parser.node.ASTMethod.execute(ASTMethod.java:
260)
at
org.apache.velocity.runtime.parser.node.ASTReference.execute(ASTReference.java:
207)
at
org.apache.velocity.runtime.parser.node.ASTReference.value(ASTReference.java:
357)
at
org.apache.velocity.runtime.parser.node.ASTSetDirective.render(ASTSetDirective.java:
135)
at
org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.java:
271)
at org.apache.velocity.Template.merge(Template.java:296)
at
org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:492)
at
org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:461)
at
org.apache.turbine.services.velocity.TurbineVelocityService.executeRequest(TurbineVelocityService.java:
415)
at
org.apache.turbine.services.velocity.TurbineVelocityService.handleRequest(TurbineVelocityService.java:
281)
at
org.apache.turbine.services.velocity.TurbineVelocity.handleRequest(TurbineVelocity.java:
71)
at
org.apache.turbine.modules.screens.VelocityScreen.buildTemplate(VelocityScreen.java:
119)
at
org.apache.turbine.modules.screens.TemplateScreen.doBuild(TemplateScreen.java:
101)
at org.apache.turbine.modules.Screen.build(Screen.java:57)
at
org.apache.turbine.modules.ScreenLoader.eval(ScreenLoader.java:104)
at
org.apache.turbine.modules.layouts.VelocityOnlyLayout.doBuild(VelocityOnlyLayout.java:
92)
at org.apache.turbine.modules.Layout.build(Layout.java:53)
at
org.apache.turbine.modules.LayoutLoader.exec(LayoutLoader.java:98)
at
org.apache.turbine.modules.pages.DefaultPage.doBuild(DefaultPage.java:
146)
at org.apache.turbine.modules.Page.build(Page.java:53)
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:
627)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:
729)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:
269)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:
188)
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:
213)
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:
172)
at
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:
433)
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:
127)
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:
117)
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:
108)
at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:
174)
at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:
875)
at org.apache.coyote.http11.Http11BaseProtocol
$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:
665)
at
org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:
528)
at
org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:
81)
at org.apache.tomcat.util.threads.ThreadPool
$ControlRunnable.run(ThreadPool.java:689)
at java.lang.Thread.run(Thread.java:619)

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

> http://groups.google.com/group/xnat_discussion/browse_thread/thread/3...

>
> I would recommend the following steps:
>

> * Backup the database using pg_dump
>
> * Run this SQL in the above post
>
> * In the webapp go to Administration -> More Options -> Clear DB Cache
>

> * Logout and log back in... maybe even restart tomcat just to make sure all caching is purged.

> > > > > > > For more options, visit this group athttp://groups.google.com/group/xnat_discussion?hl=en.
>
> > > > > > > The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
>
> > > > --
>
> > > > You received this message because you are subscribed to the Google Groups "xnat_discussion" group.
>

> > > > For more options, visit this group athttp://groups.google.com/group/xnat_discussion?hl=en.
>
> > > > The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
>
> > > --
>
> > > You received this message because you are subscribed to the Google Groups "xnat_discussion" group.
>

> > > For more options, visit this group athttp://groups.google.com/group/xnat_discussion?hl=en.
>
> > > The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
>
> > --
>
> > You received this message because you are subscribed to the Google Groups "xnat_discussion" group.
>

> > For more options, visit this group athttp://groups.google.com/group/xnat_discussion?hl=en.
>
> > The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action
>

> ...
>
> read more »

Kevin Archie

unread,

Mar 27, 2011, 10:45:30 PM3/27/11

to xnat_discussion

Alex,

The first error in the log (error starting DICOM SCP) probably
indicates that you have DicomServer 1.4.x running on that machine. The
DICOM C-STORE service is now (as of XNAT 1.5) integrated into XNAT;
your old DicomServer should be shut down so it doesn't get in the way.

- Kevin

> me()) of '==' operation has null value. If a...
>
> read more »

Olsen, Tim

unread,

Mar 28, 2011, 12:16:41 PM3/28/11

to xnat_di...@googlegroups.com

This one...

org.nrg.xft.exception.ElementNotFoundException: Element not found:
'fs:automaticSegmentationData'

Makes it look like your Database expects there to be a freesurfer schema, but it hasn't been added to your new InstanceSettings.xml.

Tim

Tim,

Thanks, Alex.

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

Logs output on login:

xdat.log:

velocity.log:

axis.log:

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

turbine.log:

velocity.log:

xdat.log:

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

xdat.log:

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

To post to this group, send email to xnat_di...@googlegroups.com.
To unsubscribe from this group, send email to xnat_discussi...@googlegroups.com.

Alex

unread,

Mar 28, 2011, 6:14:20 PM3/28/11

to xnat_discussion

I didn't add freesurfer schema to the upgraded instance yet, so I
expected to see these errors in logs.

I'm still trying to resolve the issues caused by the 1.4 bug on
upgraded instances. I followed your instructions on modifying the
database (http://groups.google.com/group/xnat_discussion/msg/
6b3bf86f0186fb68), but that didn't resolve the issues.

Alex.

> org.nrg.xnat.restlet.servlet.XNATRestletServlet.startDicomSCP(XNATRestletSe rvlet.java:
> 68)
> at
> org.nrg.xnat.restlet.servlet.XNATRestletServlet.init(XNATRestletServlet.jav a:

> org.apache.velocity.runtime.parser.node.ASTReference.execute(ASTReference.j ava:
> 207)
> at
> org.apache.velocity.runtime.parser.node.ASTReference.value(ASTReference.jav a:
> 357)
> at
> org.apache.velocity.runtime.parser.node.ASTSetDirective.render(ASTSetDirect ive.java:

> 135)
> at
> org.apache.velocity.runtime.parser.node.ASTBlock.render(ASTBlock.java:
> 94)
> at
> org.apache.velocity.runtime.parser.node.ASTIfStatement.render(ASTIfStatemen t.java:
> 109)
> at
> org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.java:
> 271)
> at org.apache.velocity.Template.merge(Template.java:296)
> at
> org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:492)
> at
> org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:461)
> at

> org.apache.turbine.services.velocity.TurbineVelocityService.executeRequest( TurbineVelocityService.java:
> 415)
> at
> org.apache.turbine.services.velocity.TurbineVelocityService.handleRequest(T urbineVelocityService.java:
> 281)
> at
> org.apache.turbine.services.velocity.TurbineVelocity.handleRequest(TurbineV elocity.java:
> 71)
> at
> org.apache.turbine.modules.navigations.VelocityNavigation.buildTemplate(Vel ocityNavigation.java:
> 100)
> at
> org.apache.turbine.modules.navigations.TemplateNavigation.doBuild(TemplateN avigation.java:

> 66)
> at org.apache.turbine.modules.Navigation.build(Navigation.java:
> 57)
> at
> org.apache.turbine.modules.NavigationLoader.eval(NavigationLoader.java:
> 104)
> at

> org.apache.turbine.util.template.TemplateNavigation.toString(TemplateNaviga tion.java:
> 106)
> at
> org.apache.velocity.runtime.parser.node.ASTReference.render(ASTReference.ja va:

> 321)
> at
> org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.java:
> 271)
> at org.apache.velocity.Template.merge(Template.java:296)
> at
> org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:492)
> at
> org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:461)
> at

> org.apache.turbine.services.velocity.TurbineVelocityService.executeRequest( TurbineVelocityService.java:
> 415)
> at
> org.apache.turbine.services.velocity.TurbineVelocityService.handleRequest(T urbineVelocityService.java:
> 281)
> at
> org.apache.turbine.services.velocity.TurbineVelocity.handleRequest(TurbineV elocity.java:
> 71)
> at
> org.apache.turbine.modules.layouts.VelocityOnlyLayout.doBuild(VelocityOnlyL ayout.java:

> 116)
> at org.apache.turbine.modules.Layout.build(Layout.java:53)
> at
> org.apache.turbine.modules.LayoutLoader.exec(LayoutLoader.java:98)
> at
> org.apache.turbine.modules.pages.DefaultPage.doBuild(DefaultPage.java:
> 146)
> at org.apache.turbine.modules.Page.build(Page.java:53)
> at org.apache.turbine.modules.PageLoader.exec(PageLoader.java:
> 98)
> at org.apache.turbine.Turbine.doGet(Turbine.java:751)
> at org.apache.turbine.Turbine.doPost(Turbine.java:846)
> at javax.servlet.http.HttpServlet.service(HttpServlet.java:
> 647)
> at javax.servlet.http.HttpServlet.service(HttpServlet.java:
> 729)
> at

> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applicatio nFilterChain.java:
> 269)
> at
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterC hain.java:
> 188)
> at
> org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.j ava:
> 213)
> at
> org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.j ava:
> 172)
> at
> org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBas e.java:

> 433)
> at
> org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:
> 127)
> at
> org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:
> 117)
> at
> org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.jav a:
> 108)
> at
> org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:
> 174)
> at
> org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:
> 875)
> at org.apache.coyote.http11.Http11BaseProtocol
> $Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:
> 665)
> at

> org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.ja va:
> 528)
> at
> org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerW orkerThread.java:

> 25)
> at java.lang.reflect.Method.invoke(Method.java:597)
> at
> org.apache.velocity.runtime.parser.node.ASTMethod.execute(ASTMethod.java:
> 260)
> at

> 135)
> at
> org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.java:
> 271)
> at org.apache.velocity.Template.merge(Template.java:296)
> at
> org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:492)
> at
> org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:461)
> at

> org.apache.turbine.modules.screens.VelocityScreen.buildTemplate(VelocityScr een.java:
> 119)
> at
> org.apache.turbine.modules.screens.TemplateScreen.doBuild(TemplateScreen.ja va:

> 101)
> at org.apache.turbine.modules.Screen.build(Screen.java:57)
> at
> org.apache.turbine.modules.ScreenLoader.eval(ScreenLoader.java:104)
> at
> org.apache.turbine.modules.layouts.VelocityOnlyLayout.doBuild(VelocityOnlyL ayout.java:
> 92)
> at org.apache.turbine.modules.Layout.build(Layout.java:53)
> at
> org.apache.turbine.modules.LayoutLoader.exec(LayoutLoader.java:98)
> at
> org.apache.turbine.modules.pages.DefaultPage.doBuild(DefaultPage.java:
> 146)
> at org.apache.turbine.modules.Page.build(Page.java:53)
> 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:
> 627)
> at javax.servlet.http.HttpServlet.service(HttpServlet.java:
> 729)
> at

> org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.ja va:
> 528)
> at
> org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerW orkerThread.java:

> 81)
> at org.apache.tomcat.util.threads.ThreadPool
> $ControlRunnable.run(ThreadPool.java:689)
> at java.lang.Thread.run(Thread.java:619)
> 2011-03-27 20:35:59,735 [http-8080-Processor19] ERROR
> org.apache.turbine.services.velocity.TurbineVelocityService - Class
> org
> .nrg.xdat.om.XnatProjectdata.getBundles threw Exception
> java.lang.NullPointerException
> at
> org.nrg.xdat.om.base.BaseXnatProjectdata.getBundles(BaseXnatProjectdata.jav a:
> 1160)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:
> 39)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImp l.java:

> 25)
> at java.lang.reflect.Method.invoke(Method.java:597)
> at
> org.apache.velocity.runtime.parser.node.ASTMethod.execute(ASTMethod.java:
> 260)
> at

> 135)
> at
> org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.java:
> 271)
> at
> org.apache.velocity.runtime.directive.Parse.render(Parse.java:232)
> at
> org.apache.velocity.runtime.parser.node.ASTDirective.render(ASTDirective.ja va:
> 153)
> at
> org.apache.velocity.runtime.parser.node.ASTBlock.render(ASTBlock.java:
> 94)
> at
> org.apache.velocity.runtime.parser.node.ASTIfStatement.render(ASTIfStatemen t.java:

> 109)
> at
> org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.java:
> 271)
> at org.apache.velocity.Template.merge(Template.java:296)
> at
> org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:492)
> at
> org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:461)
> at

> org.apache.turbine.modules.screens.VelocityScreen.buildTemplate(VelocityScr een.java:
> 119)
> at
> org.apache.turbine.modules.screens.TemplateScreen.doBuild(TemplateScreen.ja va:

> org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.ja va:
> 528)
> at
> org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerW orkerThread.java:

> 25)
> at java.lang.reflect.Method.invoke(Method.java:597)
> at
> org.apache.velocity.runtime.parser.node.ASTMethod.execute(ASTMethod.java:
> 260)
> at

> org.apache.turbine.modules.screens.VelocityScreen.buildTemplate(VelocityScr een.java:
> 119)
> at
> org.apache.turbine.modules.screens.TemplateScreen.doBuild(TemplateScreen.ja va:

> org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.ja va:
> 528)
> at
> org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerW orkerThread.java:

> 81)
> at org.apache.tomcat.util.threads.ThreadPool
> $ControlRunnable.run(ThreadPool.java:689)
> at java.lang.Thread.run(Thread.java:619)
> 2011-03-27 20:35:59,733 [http-8080-Processor19] ERROR
> org.nrg.xdat.om.base.auto.AutoXnatProjectdata -
> org.nrg.xft.exception.ElementNotFoundException: Element not found:
> 'fs:aparcRegionAnalysis'
> at
> org.nrg.xft.meta.XFTMetaManager.FindElement(XFTMetaManager.java:224)
> at
> org.nrg.xft.meta.XFTMetaManager.GetWrappedElementByName(XFTMetaManager.java :
> 368)
> at
> org.nrg.xft.schema.Wrappers.GenericWrapper.GenericWrapperElement.GetElement (GenericWrapperElement.java:
> 167)
> at
> org.nrg.xdat.om.base.BaseXnatProjectdata.getDefaultSearch(BaseXnatProjectda ta.java:
> 1246)
> at
> org.nrg.xdat.om.base.BaseXnatProjectdata.getBundles(BaseXnatProjectdata.jav a:

> 1137)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:
> 39)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImp l.java:

> 25)
> at java.lang.reflect.Method.invoke(Method.java:597)
> at
> org.apache.velocity.runtime.parser.node.ASTMethod.execute(ASTMethod.java:
> 260)
> at

> org.apache.turbine.modules.screens.VelocityScreen.buildTemplate(VelocityScr een.java:
> 119)
> at
> org.apache.turbine.modules.screens.TemplateScreen.doBuild(TemplateScreen.ja va:

> org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.ja va:
> 528)
> at
> org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerW orkerThread.java:

> 25)
> at java.lang.reflect.Method.invoke(Method.java:597)
> at
> org.apache.velocity.runtime.parser.node.ASTMethod.execute(ASTMethod.java:
> 260)
> at

> org.apache.turbine.modules.screens.VelocityScreen.buildTemplate(VelocityScr een.java:
> 119)
> at
> org.apache.turbine.modules.screens.TemplateScreen.doBuild(TemplateScreen.ja va:

> org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.ja va:
> 528)
> at
> org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerW orkerThread.java:

> 1158)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:
> 39)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImp l.java:

> 25)
> at java.lang.reflect.Method.invoke(Method.java:597)
> at
> org.apache.velocity.runtime.parser.node.ASTMethod.execute(ASTMethod.java:
> 260)
> at

> org.apache.turbine.modules.screens.VelocityScreen.buildTemplate(VelocityScr een.java:
> 119)
> at
> org.apache.turbine.modules.screens.TemplateScreen.doBuild(TemplateScreen.ja va:

> org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.ja va:
> 528)
> at
> org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerW orkerThread.java:

> 81)
> at org.apache.tomcat.util.threads.ThreadPool
> $ControlRunnable.run(ThreadPool.java:689)
> at java.lang.Thread.run(Thread.java:619)
>

> --------------------------------------------------------------------------- --------------------------------------------------------------------------- ----------------

> 25)
> at java.lang.reflect.Method.invoke(Method.java:597)
> at
> org.apache.velocity.runtime.parser.node.ASTMethod.execute(ASTMethod.java:
> 260)
> at

> org.apache.turbine.modules.screens.VelocityScreen.buildTemplate(VelocityScr een.java:
> 119)
> at
> org.apache.turbine.modules.screens.TemplateScreen.doBuild(TemplateScreen.ja va:

> org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.ja va:
> 528)
> at
> org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerW orkerThread.java:

> 81)
> at org.apache.tomcat.util.threads.ThreadPool
> $ControlRunnable.run(ThreadPool.java:689)
> at java.lang.Thread.run(Thread.java:619)
>

> --------------------------------------------------------------------------- --------------------------------------------------------------------------- ---------------------

Alex

unread,

Mar 28, 2011, 6:16:09 PM3/28/11

to xnat_discussion

Kevin,

Thank you for your input. I'm running the test instance on the same
server as the production, so the built-in dicom server is conflicting
with the stand-alone dicom server we use in production.

Alex.

> ...
>
> read more »

Archie, Kevin

unread,

Mar 29, 2011, 1:22:03 AM3/29/11

to xnat_di...@googlegroups.com

Alex,

You could set the XNAT 1.5 DICOM port (on the Default Settings page) to some other number so as not to conflict with the 1.4 installation.

- Kevin

> --
> You received this message because you are subscribed to the Google Groups "xnat_discussion" group.

> To post to this group, send email to xnat_di...@googlegroups.com.
> To unsubscribe from this group, send email to xnat_discussi...@googlegroups.com.
> For more options, visit this group at http://groups.google.com/group/xnat_discussion?hl=en.

Alex

unread,

Mar 29, 2011, 3:33:58 PM3/29/11

to xnat_discussion

Kevin,

Thanks, I did that already - no conflict.

Alex.

> ...
>
> read more »

Reply all

Reply to author

Forward

0 new messages