Installation errors

[Karen Rei Pease]

Sorry to bug you all. I'm following the installation instructions here:

http://nrg.wikispaces.com/XNAT_Source

Step 8 reads:

cd deployments/xnat/
../../bin/StoreXML -location security/security.xml -allowDataDeletion true

When I try it, I get:

[meme@fwiffo xnat]$ cd deployments/xnat/
[meme@fwiffo xnat]$ ../../bin/StoreXML -location security/security.xml
-allowDataDeletion true
Unable to connect to web service.
SETTINGS LOCATION: /home/meme/xnat/deployments/xnat/
WARNING: Data Type:cat:catalog has no columns which uniquely identify it.
WARNING: Data Type:cat:catalog_metaField has no columns which uniquely
identify it.
WARNING: Data Type:cat:catalog_tag has no columns which uniquely identify it.
WARNING: Data Type:cat:entry has no columns which uniquely identify it.
WARNING: Data Type:cat:entry_metaField has no columns which uniquely identify
it.
WARNING: Data Type:cat:entry_tag has no columns which uniquely identify it.
WARNING: Data Type:cat:dcmEntry has no columns which uniquely identify it.
WARNING: Data Type:cat:dcmCatalog has no columns which uniquely identify it.
WARNING: Data Type:xnat:statisticsData has no columns which uniquely identify
it.
WARNING: Data Type:xnat:abstractStatistics has no columns which uniquely
identify it.
WARNING: Data Type:arc:project_pipeline has no columns which uniquely identify
it.
WARNING: Data Type:arc:pathInfo has no columns which uniquely identify it.
WARNING: Data Type:wrk:abstractExecutionEnvironment has no columns which
uniquely identify it.
WARNING: Data Type:wrk:xnatExecutionEnvironment has no columns which uniquely
identify it.
WARNING: Data Type:wrk:xnatExecutionEnvironment_notify has no columns which
uniquely identify it.
Found Document:security/security.xml
XERCES - XML Document is valid
Loaded XML Item:xdat:security
Validation: PASSED
ERROR: relation "xdat_security" does not exist

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

The log is really spammy; the only thing that I see that I think may be
relevant is at the end:

2008-12-11 15:59:33,510 [main] ERROR org.nrg.xft.XFT -
org.postgresql.util.PSQLException: ERROR: relation "xdat_security" does not
exist

at
org.postgresql.util.PSQLException.parseServerError(PSQLException.java:
139)
at org.postgresql.core.QueryExecutor.executeV3(QueryExecutor.java:152)
at org.postgresql.core.QueryExecutor.execute(QueryExecutor.java:100)
at org.postgresql.core.QueryExecutor.execute(QueryExecutor.java:43)
at
org.postgresql.jdbc1.AbstractJdbc1Statement.execute(AbstractJdbc1State
ment.java:517)
at
org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2State
ment.java:50)
at
org.postgresql.jdbc1.AbstractJdbc1Statement.executeQuery(AbstractJdbc1
Statement.java:233)
at
org.postgresql.jdbc1.AbstractJdbc1Statement.executeQuery(AbstractJdbc1
Statement.java:221)
at
org.apache.commons.dbcp.DelegatingStatement.executeQuery(DelegatingSta
tement.java:205)
at org.nrg.xft.db.PoolDBUtils.executeSelectQuery(PoolDBUtils.java:401)
at org.nrg.xft.search.TableSearch.Execute(TableSearch.java:205)
at org.nrg.xft.search.ItemSearch.execute(ItemSearch.java:185)
at org.nrg.xft.search.ItemSearch.exec(ItemSearch.java:327)
at org.nrg.xft.search.ItemSearch.exec(ItemSearch.java:154)
at org.nrg.xft.XFTItem.getUniqueMatches(XFTItem.java:2441)
at org.nrg.xft.db.DBAction.StoreItem(DBAction.java:477)
at org.nrg.xft.db.DBAction.StoreItem(DBAction.java:85)
at org.nrg.xft.XFTItem.save(XFTItem.java:5993)
at org.nrg.xdat.XDATTool.storeXML(XDATTool.java:187)
at org.nrg.xdat.XDATTool.storeXML(XDATTool.java:121)
at StoreXML.process(StoreXML.java:255)
at
org.nrg.xft.commandPrompt.CommandPromptTool._process(CommandPromptTool
.java:407)
at
org.nrg.xft.commandPrompt.CommandPromptTool.run(CommandPromptTool.java
:355)
at
org.nrg.xft.commandPrompt.CommandPromptTool.<init>(CommandPromptTool.j
ava:151)
at StoreXML.<init>(StoreXML.java:45)
at StoreXML.main(StoreXML.java:49)

What does this mean?

- Karen

[Timothy Olsen]

The xdat_security table should have been created in step 7 when you executed the generated sql file.

Confirm that the database name you executed the file on matches the one specified in the build.properties file. That's a common mistake.

If that is OK, then maybe the sql failed and you missed the error message. If you execute the file using PGAdmin instead of psql, you'll get better visual description of the results (i.e. it will stop at the first error and state what the error was).

If Step 7 completes successfully, then that table should exist.

Hope this helps,
Tim

[Karen Rei Pease]

You're right -- I must have missed step 7. I ran it and then re-ran step 8,
and it succeeded. However, step 9 now fails:

Item modifications stored.
Item Successfully Stored.
[meme@fwiffo xnat]$ ../../bin/StoreXML -dir ./work/field_groups -u admin -p
admin -allowDataDeletion true

User Init(): 15ms
User(login) Loaded (90)ms
User(login,password) Loaded (90)ms
Found Document:./work/field_groups/subject_infant.xml

XERCES - XML Document is valid

Loaded XML Item:FieldDefinitionSet
Validation: PASSED
ERROR: relation "xnat_fielddefinitiongroup_field" does not exist

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

ERROR: relation "xnat_fielddefinitiongroup_field" does not exist

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

[meme@fwiffo xnat]$

I looked back at the output from step 7, and I noticed some errors, like:

CREATE FUNCTION
CREATE FUNCTION
CREATE FUNCTION
CREATE FUNCTION
CREATE FUNCTION
CREATE FUNCTION
CREATE FUNCTION
CREATE FUNCTION
CREATE FUNCTION
CREATE FUNCTION
CREATE FUNCTION
CREATE FUNCTION
psql:deployments/xnat/sql/xnat.sql:53664: ERROR: syntax error at or near "$"
atcharacter 74
psql:deployments/xnat/sql/xnat.sql:53664: ERROR: syntax error at or near "i"
atcharacter 9
psql:deployments/xnat/sql/xnat.sql:53664: ERROR: syntax error at or near "t"
atcharacter 19
psql:deployments/xnat/sql/xnat.sql:53664: ERROR: syntax error at or near
"WHILE" at character 9
psql:deployments/xnat/sql/xnat.sql:53664: ERROR: syntax error at or near "t"
atcharacter 14
psql:deployments/xnat/sql/xnat.sql:53664: ERROR: syntax error at or near
"LOOP"at character 13
psql:deployments/xnat/sql/xnat.sql:53664: ERROR: syntax error at or near
"RETURN" at character 9
psql:deployments/xnat/sql/xnat.sql:53664: WARNING: there is no transaction in
progress
COMMIT
psql:deployments/xnat/sql/xnat.sql:53664: ERROR: syntax error at or near "$"
atcharacter 2

Is it possible that my running step 8 before step 7 messed it up somehow? Do
I need to drop the xnat database, recreate it and start over? Or does this
look like a bug of some sort?

- Karen

[Timothy Olsen]

Karen,

Step 8 should not have modified the database in any way. It should have failed to do anything.

Did you try running the sql via PGAdmin? It should have made any exceptions more meaningful.

Are you building the release from the xnat_1_4b_061008 branch of the cvs repository?

[Karen Rei Pease]

I ran it with psql, like the instructions said. I don't seem to have a
program called "PGAdmin" on my computer. Should I try to track down and
install a copy?

Yes, I'm building the release from the xnat_1_4b_061008 branch of the cvs
repository.

- Karen

[Karen Rei Pease]

Just following up: I sent this reply on Friday and haven't heard back. As a
refresher, here are the errors being gotten in step 9:

> ERROR: relation "xnat_fielddefinitiongroup_field" does not exist
>
> ERROR: See log for details (logs/xdat.log).
> ERROR: relation "xnat_fielddefinitiongroup_field" does not exist
>
> ERROR: See log for details (logs/xdat.log).

I ran it with psql, like the instructions said. I don't seem to have a
program called "PGAdmin" on my computer. Should I try to track down and
install a copy?

Yes, I'm building the release from the xnat_1_4b_061008 branch of the cvs
repository.

I can do an update of the CVS tree, start from scratch, or anything else that
you think may be helpful. Thank you for your time.

- Karen

---------- Forwarded Message ----------

Subject: Re: Installation errors
Date: Friday 12 December 2008 12:30 pm
From: Karen Rei Pease <karen...@uiowa.edu>
To: xnat_di...@googlegroups.com

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

[Timothy Olsen]

Karen,

When I execute the steps in the tutorial, I don't receive this exception. So, it must be something local to your installation. What version of PostgreSQL are you running?

I would highly recommend using PGAdminIII to interact with your database. The exception management alone is worth it. It is available here: http://www.pgadmin.org/. Sometimes it comes pre-packaged with Postgres. Some versions of linux are pre-configured with it as well.

[Karen Rei Pease]

Version 7.4.19-1.el4_6.1.

I'm going to try starting over the installation from scratch, including a
fresh CVS update and using PGAdminIII like you suggest, and see how things
work out.

- Karen

[Timothy Olsen]

Karen,

We haven't tested the BETA version of XNAT on PostgreSQL 7.4. Our usage of XNAT 1.4 Beta has been limited to PostgreSQL 8.0 and up. I do hope to support PostgreSQL 7.4, but for the time being there may be issues. This could be related to that.

I would recommend retrying the steps with PGAdminIII. This should at least give you a more meaningful error message as to what is going wrong.

[Karen Rei Pease]

I did a fresh install on a different system that had Postgres 8, and it's up
and running now. Well, kind of. Whenever I try to log in as admin, on the
screen I get:

An I/O error has occured while flushing the output - Exception:
java.net.SocketException: Broken pipe Stack Trace: java.net.SocketException:
Broken pipe at java.net.SocketOutputStream.socketWrite0(Native Method) at
java.net.SocketOutputStream.socketWrite(SocketOutputStream.java:92) at
java.net.SocketOutputStream.write(SocketOutputStream.java:136) at
java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:65) at
java.io.BufferedOutputStream.flush(BufferedOutputStream.java:123) at
org.postgresql.core.PGStream.flush(PGStream.java:411) at
org.postgresql.core.QueryExecutor.sendQueryV3(QueryExecutor.java:337) at
org.postgresql.core.QueryExecutor.executeV3(QueryExecutor.java:121) at

org.postgresql.core.QueryExecutor.execute(QueryExecutor.java:100) at
org.postgresql.core.QueryExecutor.execute(QueryExecutor.java:43) at
org.postgresql.jdbc1.AbstractJdbc1Statement.execute(AbstractJdbc1Statement.java:517)
at
org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:50)
at
org.postgresql.jdbc1.AbstractJdbc1Statement.executeQuery(AbstractJdbc1Statement.java:233)
at
org.postgresql.jdbc1.AbstractJdbc1Statement.executeQuery(AbstractJdbc1Statement.java:221)
at

org.apache.commons.dbcp.DelegatingStatement.executeQuery(DelegatingStatement.java:205)

at org.nrg.xft.db.PoolDBUtils.executeSelectQuery(PoolDBUtils.java:401) at
org.nrg.xft.search.TableSearch.Execute(TableSearch.java:205) at

org.nrg.xft.search.ItemSearch.exec(ItemSearch.java:381) at
org.nrg.xft.search.ItemSearch.exec(ItemSearch.java:120) at
org.nrg.xdat.security.XDATUser.(XDATUser.java:93) at
org.nrg.xdat.security.XDATUser.(XDATUser.java:133) at
org.nrg.xdat.turbine.modules.actions.XDATLoginUser.doPerform(XDATLoginUser.java:80)
at
org.apache.turbine.modules.actions.VelocityAction.doPerform(VelocityAction.java:46)
at
org.apache.turbine.util.velocity.VelocityActionEvent.perform(VelocityActionEvent.java:82)
at
org.apache.turbine.modules.actions.VelocityAction.perform(VelocityAction.java:72)
at org.apache.turbine.modules.ActionLoader.exec(ActionLoader.java:96) at
org.apache.turbine.modules.pages.DefaultPage.doBuild(DefaultPage.java:113) 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:637) at
javax.servlet.http.HttpServlet.service(HttpServlet.java:717) at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
at
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:433)
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:128)
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:286)
at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:845)
at
org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:583)
at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:447) at
java.lang.Thread.run(Thread.java:619) End of Stack Trace

Any clue what this means? Also, is this supposed to be showing up on the
screen, rather than in catalina.out? In general you hide stacktraces from
end-users so as to make it harder for attackers to exploit errors.

- Karen

[Timothy Olsen]

This usually means Tomcat cannot connect to PostgreSQL. Sometimes this occurs when PostgreSQL is rebooted. In that and previous versions of XNAT, Tomcat must be rebooted whenever PostgreSQL is restarted. If PostgreSQL is up, then try restarting Tomcat and see if that clears it up.

This is the only exception which should show up that way. It is a fatal error. Generally if its showing up in a production environment, you have bigger issues then what a hacker may think. Just the same, you are correct that it should be hidden.

In my more recent development code, this message is being better concealed. Also, in my more recent version the server would attempt to re-connect to PostgreSQL after its connections have been broken. These improvements will be in the official release of 1.4.

[Karen Rei Pease]

Thanks for the tip -- that did the trick. :)

- Karen

>java:517) at
> org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.
>java:50) at
> org.postgresql.jdbc1.AbstractJdbc1Statement.executeQuery(AbstractJdbc1State
>ment.java:233) at
> org.postgresql.jdbc1.AbstractJdbc1Statement.executeQuery(AbstractJdbc1State
>ment.java:221) at
> org.apache.commons.dbcp.DelegatingStatement.executeQuery(DelegatingStatemen
>t.java:205) at

[Karen Rei Pease]

Unfortunately, right after that, on the first page it brings me to, I can't
get out of it. It asks me to configure my default settings. No matter what
I put, I can't get out of this page -- by clicking save, by clicking other
links, etc. In the xdat.log, I see:

2008-12-17 10:32:10,488 [http-7080-2] ERROR
org.nrg.xdat.om.base.auto.AutoArcPath
info - java.lang.NullPointerException

What does this mean?

- Karen

On Tuesday 16 December 2008 08:42 pm, Timothy Olsen wrote:

>java:517) at
> org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.
>java:50) at
> org.postgresql.jdbc1.AbstractJdbc1Statement.executeQuery(AbstractJdbc1State
>ment.java:233) at
> org.postgresql.jdbc1.AbstractJdbc1Statement.executeQuery(AbstractJdbc1State
>ment.java:221) at
> org.apache.commons.dbcp.DelegatingStatement.executeQuery(DelegatingStatemen
>t.java:205) at

> org.nrg.xft.db.PoolDBUtils.executeSelectQuery(PoolDBUtils.java:401) at
> org.nrg.xft.search.TableSearch.Execute(TableSearch.java:205) at
> org.nrg.xft.search.ItemSearch.exec(ItemSearch.java:381) at
> org.nrg.xft.search.ItemSearch.exec(ItemSearch.java:120) at
> org.nrg.xdat.security.XDATUser.(XDATUser.java:93) at
> org.nrg.xdat.security.XDATUser.(XDATUser.java:133) at

> org.nrg.xdat.turbine.modules.actions.XDATLoginUser.doPerform(XDATLoginUser.
>java:80) at
> org.apache.turbine.modules.actions.VelocityAction.doPerform(VelocityAction.
>java:46) at
> org.apache.turbine.util.velocity.VelocityActionEvent.perform(VelocityAction
>Event.java:82) at
> org.apache.turbine.modules.actions.VelocityAction.perform(VelocityAction.ja

>va:72) at org.apache.turbine.modules.ActionLoader.exec(ActionLoader.java:96)
> at
> org.apache.turbine.modules.pages.DefaultPage.doBuild(DefaultPage.java:113)
> 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:637) at
> javax.servlet.http.HttpServlet.service(HttpServlet.java:717) at

> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applicatio
>nFilterChain.java:290) at
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterC
>hain.java:206) at
> org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.j
>ava:233) at
> org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.j
>ava:191) at
> org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBas
>e.java:433) at
> org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:12
>8) at
> org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:10
>2) at
> org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.jav

> > > > org.postgresql.jdbc1.AbstractJdbc1Statement.execute(AbstractJdbc1Stat
> > > >e ment.java:517)
> > > > at
> > > > org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Stat
> > > >e ment.java:50)
> > > > at
> > > > org.postgresql.jdbc1.AbstractJdbc1Statement.executeQuery(AbstractJdbc
> > > >1 Statement.java:233)
> > > > at
> > > > org.postgresql.jdbc1.AbstractJdbc1Statement.executeQuery(AbstractJdbc
> > > >1 Statement.java:221)
> > > > at
> > > > org.apache.commons.dbcp.DelegatingStatement.executeQuery(DelegatingSt

> > > >a tement.java:205)
> > > > at
> > > > org.nrg.xft.db.PoolDBUtils.executeSelectQuery(PoolDBUtils.java:401)
> > > > at org.nrg.xft.search.TableSearch.Execute(TableSearch.java:205) at
> > > > org.nrg.xft.search.ItemSearch.execute(ItemSearch.java:185) at
> > > > org.nrg.xft.search.ItemSearch.exec(ItemSearch.java:327) at
> > > > org.nrg.xft.search.ItemSearch.exec(ItemSearch.java:154) at
> > > > org.nrg.xft.XFTItem.getUniqueMatches(XFTItem.java:2441) at
> > > > org.nrg.xft.db.DBAction.StoreItem(DBAction.java:477)
> > > > at org.nrg.xft.db.DBAction.StoreItem(DBAction.java:85)
> > > > at org.nrg.xft.XFTItem.save(XFTItem.java:5993)
> > > > at org.nrg.xdat.XDATTool.storeXML(XDATTool.java:187)
> > > > at org.nrg.xdat.XDATTool.storeXML(XDATTool.java:121)
> > > > at StoreXML.process(StoreXML.java:255)
> > > > at

> > > > org.nrg.xft.commandPrompt.CommandPromptTool._process(CommandPromptToo
> > > >l .java:407)
> > > > at
> > > > org.nrg.xft.commandPrompt.CommandPromptTool.run(CommandPromptTool.jav
> > > >a
> > > >
> > > > :355)
> > > >
> > > > at
> > > > org.nrg.xft.commandPrompt.CommandPromptTool.<init>(CommandPromptTool.

[Timothy Olsen]

Karen,

Are you putting values in every field? All fields on that form are required.

[Karen Rei Pease]

Didn't realize they were all required, and there was no error message.
Thanks!

- Karen

> > org.postgresql.jdbc1.AbstractJdbc1Statement.execute(AbstractJdbc1Statemen
> >t. java:517) at
> > org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statemen
> >t. java:50) at
> > org.postgresql.jdbc1.AbstractJdbc1Statement.executeQuery(AbstractJdbc1Sta
> >te ment.java:233) at
> > org.postgresql.jdbc1.AbstractJdbc1Statement.executeQuery(AbstractJdbc1Sta
> >te ment.java:221) at
> > org.apache.commons.dbcp.DelegatingStatement.executeQuery(DelegatingStatem
> >en t.java:205) at

[Karen Rei Pease]

From the Tutorial:

--------------------
"ACTIONS: Click on the ‘Administration’ link. This will list all of the
loaded user accounts.

Click on the ‘admin’ link. This brings up the user report for the admin
account.

Click on the ‘Change Permissions’ link on the right. This brings up the edit
permissions page.

At the bottom of the screen, the current data types will be listed. Click on
the plus signs next to the data types. Check the boxes for Create, Read, and
Edit for the investigators. (This will give the admin account Create, Read
and Edit privileges for data of this type belonging to this investigator).
(Additional data types and investigators can be added through the
administration section). Click Submit. "
--------------------

"Administration" isn't a link. When I click on it, it just collapses the
options box. There is no "admin" link. There are "manage users" and "manage
data types" links, but I searched through them and couldn't find any page
with "plus signs". I used the "search" box for "change permissions", but it
found nothing.

The tutorial says to do this if any data types are listed as "secured", which
all but one are. Is this information out of date or am I doing something
wrong?

- Karen

> > > org.postgresql.jdbc1.AbstractJdbc1Statement.execute(AbstractJdbc1Statem
> > >en t. java:517) at
> > > org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statem
> > >en t. java:50) at
> > > org.postgresql.jdbc1.AbstractJdbc1Statement.executeQuery(AbstractJdbc1S
> > >ta te ment.java:233) at
> > > org.postgresql.jdbc1.AbstractJdbc1Statement.executeQuery(AbstractJdbc1S
> > >ta te ment.java:221) at
> > > org.apache.commons.dbcp.DelegatingStatement.executeQuery(DelegatingStat

> > > > > >2) at

> > > > > > org.postgresql.core.QueryExecutor.execute(QueryExecutor.java:100)
> > > > > > at
> > > > > > org.postgresql.core.QueryExecutor.execute(QueryExecutor.java:43)
> > > > > > at
> > > > > > org.postgresql.jdbc1.AbstractJdbc1Statement.execute(AbstractJdbc1

[Timothy Olsen]

Karen,

The version of XNAT which you checked out of CVS is a Beta version of the upcoming 1.4 release. We are still finalizing a few features, fixing numerous bugs and then rewriting much of the old documentation.

The documentation available on the www.xnat.org site is for the last publically released version (1.3). The application has changed considerably since then. I've been gradually populating some documentation on our wiki site http://nrg.wikispaces.org. However, even this has been problematic as many of the screen shots are already out of date.

Using the Beta version will require some patience and perseverance. That said, many users are using it effectively (although most of them were users of XNAT 1.3 previously), including some at U of IOWA.

Did you find the section you quoted on the WIKI or on the www.xnat.org documentation? If its in the WIKI, I'll need to correct it. If its on the www.xnat.org site then it is intended for version 1.3 and will not match version 1.4 (although may still be informative with a little patience).

FYI, when setting up from CVS, you need to follow the tutorial on the WIKI site, rather than on the www.xnat.org site. Not all of the steps on www.xnat.org are applicable for the new version. Also, it contains helpful hints (like stating that all fields on the Default Settings Form are required).

I apologize for the confusing state of things. Once 1.4 is released, we'll be able to eliminate the 1.3 documentation and things should be more straight forward.

[Karen Rei Pease]

No problem; the wiki version seems much better; I just hadn't seen it before,
and had been using the one on the website. Thanks for your help; everything
seems to be properly installed and setup now, so I can get to work trying to
get our data in. :)

- Karen

On Wednesday 17 December 2008 12:38 pm, Timothy Olsen wrote:
> Karen,
>

> > > > org.postgresql.jdbc1.AbstractJdbc1Statement.execute(AbstractJdbc1Stat
> > > >em en t. java:517) at
> > > > org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Stat
> > > >em en t. java:50) at
> > > > org.postgresql.jdbc1.AbstractJdbc1Statement.executeQuery(AbstractJdbc
> > > >1S ta te ment.java:233) at
> > > > org.postgresql.jdbc1.AbstractJdbc1Statement.executeQuery(AbstractJdbc
> > > >1S ta te ment.java:221) at
> > > > org.apache.commons.dbcp.DelegatingStatement.executeQuery(DelegatingSt

[Karen Rei Pease]

I'm going through a basic procedure to upload some test data. I've got the
data in the prearchive and I'm attempting to archive it. Part of the process
is to create a subject. So, I click to create a new subject, fill it out,
and then submit it. The window closes and I get a dialog that simply says,
"Failed to load subjects". The subject combobox gets grayed out. If I
reload the page, I can see my subject in the combobox,but selecting it
doesn't make the red check by the subject field turn green.

Is this a bug?

Lots of errors in the logs. Example:

2008-12-18 14:25:25,710 [http-7080-2] ERROR org.nrg.xdat.search.DisplaySearch
-
org.nrg.xdat.collections.DisplayFieldCollection$DisplayFieldNotFoundException:
Di
splay Field not found: 'INVEST'
at
org.nrg.xdat.collections.DisplayFieldCollection.getDisplayFieldWExcept
ion(DisplayFieldCollection.java:50)
at
org.nrg.xdat.schema.SchemaElement.getDisplayField(SchemaElement.java:8
1)
at
org.nrg.xdat.display.DisplayFieldRef.getDisplayField(DisplayFieldRef.j
ava:101)
at
org.nrg.xdat.search.DisplaySearch.convertToStoredSearch(DisplaySearch.
java:1809)
at
org.nrg.xdat.om.base.BaseXnatProjectdata.getDefaultSearch(BaseXnatProj
ectdata.java:1539)
at
org.nrg.xnat.restlet.resources.ProjectSubjectList.getRepresentation(Pr
ojectSubjectList.java:177)
at org.restlet.resource.Resource.handleGet(Resource.java:463)
at org.restlet.Finder.handle(Finder.java:351)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Router.handle(Router.java:502)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Filter.doHandle(Filter.java:150)
at com.noelios.restlet.StatusFilter.doHandle(StatusFilter.java:130)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at com.noelios.restlet.ChainHelper.handle(ChainHelper.java:124)
at
com.noelios.restlet.application.ApplicationHelper.handle(ApplicationHe
lper.java:112)
at org.restlet.Application.handle(Application.java:342)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Router.handle(Router.java:502)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Router.handle(Router.java:502)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at com.noelios.restlet.ChainHelper.handle(ChainHelper.java:124)
at org.restlet.Component.handle(Component.java:888)
at org.restlet.Server.handle(Server.java:331)
at com.noelios.restlet.ServerHelper.handle(ServerHelper.java:68)
at
com.noelios.restlet.http.HttpServerHelper.handle(HttpServerHelper.java
:147)
at
com.noelios.restlet.ext.servlet.ServerServlet.service(ServerServlet.ja
va:790)

at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Appli
cationFilterChain.java:290)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFi

lterChain.java:206)

at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperVa
lve.java:233)
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextVa

lve.java:191)

at
org.apache.catalina.authenticator.AuthenticatorBase.invoke(Authenticat
orBase.java:433)
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.ja
va:128)
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.ja
va:102)
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValv
e.java:109)
at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java
:286)
at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:
845)
at
org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.proces
s(Http11Protocol.java:583)
at

org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:447
)
at java.lang.Thread.run(Thread.java:619)

- Karen

[Karen Rei Pease]

Just as a followup: I've tried the upload on another person's xnat install,
and the same thing happens. The other person thought it looked like a bug to
them as well. Should I file this as a bug, or is there something being done
wrong here?

- Karen

[Timothy Olsen]

Karen,

I've been unable to verify that this is an issue in the June version (061108). Did you migrate to a different version?

Tim

-----Original Message-----
From: xnat_di...@googlegroups.com [mailto:xnat_di...@googlegroups.com] On Behalf Of Karen Rei Pease
Sent: Monday, December 22, 2008 12:48 PM
To: xnat_di...@googlegroups.com

[Karen Rei Pease]

Yes, we're both on the 11-19-08 version.

- Karen

[Timothy Olsen]

Karen,

I'm unable to reproduce this in a build of that branch. I may have fixed this at some point. Is your installation up to date? When was it checked out of CVS?

Tim
-----Original Message-----
From: xnat_di...@googlegroups.com [mailto:xnat_di...@googlegroups.com] On Behalf Of Karen Rei Pease

Sent: Monday, December 22, 2008 1:05 PM
To: xnat_di...@googlegroups.com

[Karen Rei Pease]

Friday. Perhaps it's the dataset I'm using? Would you like me to host it
somewhere so you can try it out?

- Karen

[Timothy Olsen]

Karen,

The images should be a separate issue. This section of the form should not be effected by the images.

Just to be sure, you could attempt creating a project on http://central.xnat.org and uploading the files there. See if you find the same bug.

[Karen Rei Pease]

I'm getting different issues on your site just trying to get to that point.
I'm getting "ERROR 200: Failure to parse experiment list" in the middle of my
upload. Username 'kpease', project 'Test'.

- Karen

> > > > org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Appl
> > > >i cationFilterChain.java:290)
> > > > at
> > > > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationF
> > > >i lterChain.java:206)
> > > > at
> > > > org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperV
> > > >a lve.java:233)
> > > > at
> > > > org.apache.catalina.core.StandardContextValve.invoke(StandardContextV
> > > >a lve.java:191)
> > > > at
> > > > org.apache.catalina.authenticator.AuthenticatorBase.invoke(Authentica

> > > >t orBase.java:433)
> > > > at
> > > > org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.j
> > > >a va:128)
> > > > at
> > > > org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.j
> > > >a va:102)

> > > > at
> > > > org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineVal
> > > >v e.java:109)
> > > > at
> > > > org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.jav
> > > >a
> > > >

> > > > :286)
> > > >
> > > > at
> > > > org.apache.coyote.http11.Http11Processor.process(Http11Processor.java
> > > >: 845)
> > > > at

> > > > org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.proce
> > > >s s(Http11Protocol.java:583)
> > > > at
> > > > org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:44

[Timothy Olsen]

Karen,

What browser are you using (including version #)?