RE: [XNAT Discussion] image uploading failure (XNAT 1.6.2)

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Herrick, Rick

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Sep 24, 2013, 6:13:36 PM9/24/13
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This is a known bug in 1.6.2.1. We have a fix in our dev tip, but the easy fix on 1.6.2.1 is to nuke the prearchive table, which is described on another discussion group posting:

 

https://groups.google.com/d/msg/xnat_discussion/PKzKTZFLYYg/z0rMteFdm4AJ

 

It’s always a good idea to search for error messages on the discussion group before posting, since often they’ve already come up for someone else and you can find the solution right away.

 

Rick Herrick

Sr. Programmer/Analyst

Neuroinformatics Research Group

Washington University School of Medicine

(314) 827-4250

 

From: xnat_di...@googlegroups.com [mailto:xnat_di...@googlegroups.com] On Behalf Of fd...@research.baycrest.org
Sent: Tuesday, September 24, 2013 9:25 AM
To: xnat_di...@googlegroups.com
Subject: [XNAT Discussion] image uploading failure (XNAT 1.6.2)

 

Hi there,

 

We have recently upgrade the xnat 1.5.4 to 1.6.2 and encountered the errors when uploading images to prearchive.  I would highly appreciate if anyone can give us a hint.

 

The upload screen prints the following messages:

 

Extraction / Review summary:

Importing file (spred_demo_data.zip)

mkdir /usr/xnat/spred/cachearchive/2/uploads/2/20130924_101630151

Uploading to /usr/xnat/spred/cachearchive/2/uploads/2/20130924_101630151/spred_demo_data.zip ...

file uploaded

mkdir /usr/xnat/spred/prearchive/ep/20130924_101630151

Importing to /usr/xnat/spred/prearchive/ep/20130924_101630151

processing

looking for DICOM files

found 192 DICOM files

found DICOM study 12_Chn_QC (1.3.12.2.1107.5.2.32.35120.30000013011512520173400000001)

done finding DICOM

looking for ECAT files

found 0 ECAT files

done finding ECAT

done

Setting additional values for 'my_data'

Successfully uploaded 1 sessions to the prearchive.

org.postgresql.util.PSQLException: ERROR: INSERT has more expressions than target columns Position: 86

 

ERROR: The process could not be completed due to exceptions - 

 

org.postgresql.util.PSQLException: ERROR: INSERT has more expressions than target columns Position: 86Your data may be available in the prearchive for your review.

 

 

The prearchive log printed logs of exceptions, just to give a few.

 

2013-09-24 10:09:56,674 [http-8080-1] ERROR org.nrg.xdat.turbine.modules.screens.SecureScreen - 

org.postgresql.util.PSQLException: The column index is out of range: 14, number of columns: 13.

            at org.postgresql.jdbc2.AbstractJdbc2ResultSet.checkColumnIndex(AbstractJdbc2ResultSet.java:2680)

            at org.postgresql.jdbc2.AbstractJdbc2ResultSet.checkResultSet(AbstractJdbc2ResultSet.java:2697)

            at org.postgresql.jdbc2.AbstractJdbc2ResultSet.getBoolean(AbstractJdbc2ResultSet.java:1889)

            at org.apache.commons.dbcp.DelegatingResultSet.getBoolean(DelegatingResultSet.java:177)

            at org.nrg.xnat.helpers.prearchive.DatabaseSession$ColType$5.getFromResult(DatabaseSession.java:384)

            at org.nrg.xnat.helpers.prearchive.DatabaseSession.getFromResult(DatabaseSession.java:761)

            at org.nrg.xnat.helpers.prearchive.PrearcDatabase.convertRStoList(PrearcDatabase.java:1717)

            at org.nrg.xnat.helpers.prearchive.PrearcDatabase.access$1000(PrearcDatabase.java:44)

            at org.nrg.xnat.helpers.prearchive.PrearcDatabase$33.op(PrearcDatabase.java:1631)

            at org.nrg.xnat.helpers.prearchive.PrearcDatabase$33.op(PrearcDatabase.java:1626)

            at org.nrg.xnat.helpers.prearchive.PrearcDatabase$SessionOp.run(PrearcDatabase.java:1797)

            at org.nrg.xnat.helpers.prearchive.PrearcDatabase.buildRows(PrearcDatabase.java:1626)

            at org.nrg.xnat.helpers.prearchive.PrearcDatabase.buildRows(PrearcDatabase.java:1703)

            at org.nrg.xnat.turbine.modules.screens.Index.doBuildTemplate(Index.java:62)

            at org.nrg.xdat.turbine.modules.screens.SecureScreen.doBuildTemplate(SecureScreen.java:175)

            at org.apache.turbine.modules.screens.TemplateScreen.doBuild(TemplateScreen.java:100)

            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:617)

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

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

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

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

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

 

 

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