scan upload error

29 views
Skip to first unread message

Miklos Espak

unread,
Apr 11, 2013, 11:59:53 AM4/11/13
to xnat_di...@googlegroups.com, Cash, David, Leung, Kelvin
Hi,

I created a script to upload NIFTI files with curl. The script creates the session and the scan, but it fails at the actual upload of the image. The error started happening recently, earlier I could upload scans with the same script.

The upload command:


The error on the stdout:

<html>
<head>
   <title>Status page</title>
</head>
<body>
<h3>Unable to identify scan</h3><p>You can get technical details <a href="http://www.w3.org/Protocols/rfc2616/rfc2616-sec10.html#sec10.4.5">here</a>.<br>
Please continue your visit at our <a href="/">home page</a>.
</p>
</body>
</html>

And the error in the application log:

ERROR:  column "nifti" does not exist at character 241
STATEMENT:  SELECT DISTINCT ON (xnat_abstractResource6)  * FROM (SELECT * FROM (SELECT xnat_abstractResource.xnat_abstractresource_id AS xnat_abstractResource6 FROM xnat_abstractResource xnat_abstractResource) SEARCH  WHERE 
( (xnat_abstractResource6=NIFTI))) SEARCH


Does anybody have an idea what is this NIFTI column and why is it missing?

I just upgraded XNAT to the latest version in the hg repo, and updated the database.

Any help would be appreciated!

Cheers,
Miklos


Miklos Espak

unread,
Apr 11, 2013, 12:05:01 PM4/11/13
to xnat_di...@googlegroups.com, Cash, David, Leung, Kelvin
I was not precise, that error is from the postgresql log.

The application.log contains an unrelated error 


and the xdat.log contains this:

2013-04-11 16:56:59,082 [http-443-5] ERROR org.nrg.xdat.om.base.auto.AutoXnatAbstractresource - 
org.postgresql.util.PSQLException: ERROR: column "nifti" does not exist
  Position: 241
at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2102)
at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1835)
at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:257)
at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:500)
at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:374)
at org.postgresql.jdbc2.AbstractJdbc2Statement.executeQuery(AbstractJdbc2Statement.java:254)
at org.apache.commons.dbcp.DelegatingStatement.executeQuery(DelegatingStatement.java:205)
at org.nrg.xft.db.PoolDBUtils.executeQuery(PoolDBUtils.java:890)
at org.nrg.xft.db.PoolDBUtils.executeSelectQuery(PoolDBUtils.java:414)
at org.nrg.xft.search.TableSearch.Execute(TableSearch.java:103)
at org.nrg.xft.search.ItemSearch.getIdentifierResults(ItemSearch.java:323)
at org.nrg.xft.search.ItemSearch.exec(ItemSearch.java:435)
at org.nrg.xft.search.ItemSearch.exec(ItemSearch.java:121)
at org.nrg.xft.search.ItemSearch.GetItems(ItemSearch.java:775)
at org.nrg.xdat.om.base.auto.AutoXnatAbstractresource.getXnatAbstractresourcesByXnatAbstractresourceId(AutoXnatAbstractresource.java:288)
at org.nrg.xnat.restlet.resources.files.FileList.<init>(FileList.java:99)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:525)
at org.restlet.Finder.createTarget(Finder.java:181)
at org.restlet.Finder.createTarget(Finder.java:226)
at org.restlet.Finder.findTarget(Finder.java:240)
at org.restlet.Finder.handle(Finder.java:329)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Router.handle(Router.java:504)
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.Router.handle(Router.java:504)
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(ApplicationHelper.java:112)
at org.restlet.Application.handle(Application.java:341)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Router.handle(Router.java:504)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Router.handle(Router.java:504)
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 org.restlet.Component.handle(Component.java:673)
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.java:881)
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.nrg.xnat.restlet.util.UpdateExpirationCookie.doFilter(UpdateExpirationCookie.java:34)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:369)
at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:109)
at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:83)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)
at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:97)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)
at org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:100)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)
at org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:78)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)
at org.nrg.xnat.security.XnatArcSpecFilter.doFilter(XnatArcSpecFilter.java:31)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)
at org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:54)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)
at org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:35)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)
at org.nrg.xnat.security.XnatBasicAuthenticationFilter.doFilter(XnatBasicAuthenticationFilter.java:118)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)
at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:187)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)
at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:105)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)
at org.springframework.security.web.session.ConcurrentSessionFilter.doFilter(ConcurrentSessionFilter.java:109)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)
at org.nrg.xnat.security.XnatExpiredPasswordFilter.doFilter(XnatExpiredPasswordFilter.java:128)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)
at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:79)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)
at org.springframework.security.web.access.channel.ChannelProcessingFilter.doFilter(ChannelProcessingFilter.java:109)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)
at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:168)
at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:237)
at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:167)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:470)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
at org.apache.catalina.valves.RequestFilterValve.process(RequestFilterValve.java:338)
at org.apache.catalina.valves.RemoteHostValve.invoke(RemoteHostValve.java:81)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:293)
at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:861)
at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:606)
at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489)
at java.lang.Thread.run(Thread.java:722)


Tim Olsen

unread,
Apr 11, 2013, 12:40:12 PM4/11/13
to xnat_di...@googlegroups.com, Cash, David, Leung, Kelvin

This looks like a bug in the SQL.  No column is missing.

 

What version did you just upgrade from?  And you just updated to the tip of the development line (xnat_builder_1_6dev)?  Sounds like a bug may have been introduced there.

 

Tim

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

Miklos Espak

unread,
Apr 11, 2013, 12:43:32 PM4/11/13
to xnat_di...@googlegroups.com, Cash, David, Leung, Kelvin
Hi Tim,

I just upgraded to the tip hoping that it solves this issue. The previous version was also ahead of 1.6.1 but cannot tell exactly which revision, but it did not work either.

Cheers,
Miklos

Miklos Espak

unread,
Apr 11, 2013, 5:57:12 PM4/11/13
to xnat_di...@googlegroups.com, Cash, David, Leung, Kelvin
By the way, do you think, it's safe to *downgrade* to the latest stable release?
Can it cause problems with the database schema, or there have been only incremental changes?

I'm not sure if this is an actual bug in the xnat_1_6dev branch or something is wrong in my database.

What do you think?

Cheers,
Miklos

Reply all
Reply to author
Forward
0 new messages