Custom Variables problem
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A. S.
May 21, 2013, 10:53:55 AM5/21/13
to xnat_di...@googlegroups.com
Hi,
followed by the listing of the attributes:
and a very big SQL-command in ==> /var/lib/tomcat6/webapps/xnat/logs/sql.log <==
we are trying to set up some custom variables for the subjects (phenotypic data, about 350 additional attributes).
everything works fine so far, the generated XML file can be uploaded and spreadsheet (csv) upload works too.
there is only one problem: after the upload of the spreadsheet the listing of the subjects fails:
"Failed to create search results."
The log-files:
==> /var/lib/tomcat6/webapps/xnat/logs/xdat.log <==2013-05-21 16:43:52,564 [http-8080-29] ERROR org.nrg.xdat.om.base.auto.AutoXnatAbstractresource -org.postgresql.util.PSQLException: ERROR: column "notifications" 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.GeneratedConstructorAccessor118.newInstance(Unknown Source) 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 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: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:68) 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$VirtualFilterChain.doFilter(FilterChainProxy.java:381) at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:168) at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:237) at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:167) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191) at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:470) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:293) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:859) at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:602) at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489) at java.lang.Thread.run(Thread.java:722)
followed by the listing of the attributes:
==> /var/lib/tomcat6/logs/catalina.out <==LOADED xnat:subjectData/fields/field[name=ID]/fieldLOADED xnat:subjectData/fields/field[name=Group]/fieldLOADED xnat:subjectData/fields/field[name=Gender]/fieldLOADED xnat:subjectData/fields/field[name=Hand]/fieldLOADED xnat:subjectData/fields/field[name=Height]/field.....
etc.and a very big SQL-command in ==> /var/lib/tomcat6/webapps/xnat/logs/sql.log <==
after that follows an PSQLException:
==> /var/lib/tomcat6/webapps/xnat/logs/restlet.log <==2013-05-21 16:43:54,712 [http-8080-36] ERROR org.nrg.xnat.restlet.resources.search.SearchResource - Failed POSTorg.postgresql.util.PSQLException: ERROR: syntax error at or near "AS" Position: 1573 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.execute(AbstractJdbc2Statement.java:366) at org.apache.commons.dbcp.DelegatingStatement.execute(DelegatingStatement.java:261) at org.nrg.xft.db.PoolDBUtils.execute(PoolDBUtils.java:914) at org.nrg.xft.db.PoolDBUtils.executeNonSelectQuery(PoolDBUtils.java:325) at org.nrg.xft.db.PoolDBUtils.ExecuteNonSelectQuery(PoolDBUtils.java:352) at org.nrg.xft.db.MaterializedView.save(MaterializedView.java:411) at org.nrg.xnat.restlet.resources.search.SearchResource.handlePost(SearchResource.java:244) at org.restlet.Finder.handle(Finder.java:357) 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 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: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$VirtualFilterChain.doFilter(FilterChainProxy.java:381) at org.nrg.xnat.security.XnatExpiredPasswordFilter.doFilter(XnatExpiredPasswordFilter.java:68) at org.springframework.security.web.FilterChainProxy$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:102) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:293) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:859) at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:602) at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489) at java.lang.Thread.run(Thread.java:722)
It is almost impossible to localize the error in a SQL-string with approx. 180,000 characters.
Could the length of the SQL-query be the problem? or the number of the custom variables? maybe a known issue?
greets,
AS
A. S.
May 21, 2013, 11:06:13 AM5/21/13
to xnat_di...@googlegroups.com
sorry,
I found the problem directly after posting the issue:
the variable "MR count" is not escaped in the SQL-statement (blank between MR and count):
[...] XNAT_SUBJECTDATA_FIELD_MAP_mr count AS XNAT_SUBJECTDATA_FIELD_MAP_mr count,[...]
that is the reason why the whole statement fails..
greets,
AS
Tim Olsen
May 21, 2013, 11:31:45 AM5/21/13
to xnat_di...@googlegroups.com
One additional note, the first error you found:
org.postgresql.util.PSQLException: ERROR: column "notifications" does not exist
Has been resolved on the tip of XNAT 1.6 dev, and will be fixed in 1.6.2.
Tim
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A. S.
May 21, 2013, 11:58:36 AM5/21/13
to xnat_di...@googlegroups.com
thanks,
just pulled from the dev, it is working now.
I also noticed that even if I can see the value of the variables in Subject Details, they all are empty on the subject listing page.
any suggestions?
AS
Tim Olsen
May 21, 2013, 12:18:45 PM5/21/13
to xnat_di...@googlegroups.com
One thing that is easy to miss with the custom variables is that I think it automatically lower-cases all of the custom variable names. I’m going off of old memories here, but I think that is what it did. So, you may want to play with changing the capitalization of your variable names to be all lower case, and see if that works as expected.
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