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#126 fixed exception after importing subjects sheet work@… business@…

After importing the example subjects sheet, I got an error:

Grails Runtime Exception Error Details Error 500: Executing action [savePostview] of controller [dbnp.importer.ImporterController?] caused exception: null identifier Servlet: grails URI: /gscf-0.5.0-demo/grails/importer/savePostview.dispatch Exception Message: null identifier Caused by: null identifier Class: ImporterController? At Line: [272] Code Snippet: Stack Trace

org.hibernate.AssertionFailure?: null identifier

at dbnp.importer.ImporterService?.saveDatamatrix(ImporterService?.groovy:245)

at dbnp.importer.ImporterService?$$FastClassByCGLIB$$3550d3b5.invoke(<generated>)

at net.sf.cglib.proxy.MethodProxy?.invoke(MethodProxy?.java:149)

at dbnp.importer.ImporterService?$$EnhancerByCGLIB$$5baed70a.saveDatamatrix(<generated>)

at GrailsMelodyGrailsPlugin?$_closure5_closure18_closure19.doCall(GrailsMelodyGrailsPlugin?.groovy:156)

at dbnp.importer.ImporterController?$_closure9.doCall(ImporterController?.groovy:272)

at dbnp.importer.ImporterController?$_closure9.doCall(ImporterController?.groovy)

at net.bull.javamelody.JspWrapper?.invoke(JspWrapper?.java:116)

at net.bull.javamelody.JdbcWrapper?$DelegatingInvocationHandler?.invoke(JdbcWrapper?.java:250)

at $Proxy30.forward(Unknown Source)

at org.apache.shiro.web.servlet.ShiroFilter?.executeChain(ShiroFilter?.java:687)

at org.apache.shiro.web.servlet.ShiroFilter?.doFilterInternal(ShiroFilter?.java:616)

at org.apache.shiro.web.servlet.OncePerRequestFilter?.doFilter(OncePerRequestFilter?.java:81)

at net.bull.javamelody.MonitoringFilter?.doFilter(MonitoringFilter?.java:388)

at org.apache.jk.server.JkCoyoteHandler?.invoke(JkCoyoteHandler?.java:190)

at org.apache.jk.common.HandlerRequest?.invoke(HandlerRequest?.java:291)

at org.apache.jk.common.ChannelSocket?.invoke(ChannelSocket?.java:769)

at org.apache.jk.common.ChannelSocket?.processConnection(ChannelSocket?.java:698)

at org.apache.jk.common.ChannelSocket?$SocketConnection?.runIt(ChannelSocket?.java:891)


#127 wontfix take into account ontology versioning, make more use of Ontocat business@…

Problem that originally raised versioning: When I click add more... to add more terms to the Compound ontology in the GSCF demo instance on, the new compounds do not show up in the list afterwards. This works with a local installation.

  • Implement ontology versioning
  • Use Ontocat instead of going direct to BioPortal?, to be able to include more ontologies and also profit from other things done in Ontocat (e.g. when NCBO changes its webservices again)
#128 fixed exception after defining a study, cannot save the study work@… business@…

When creating a study with some generated samples, a popup box is shown with an exception:

exception → org.springframework.dao.DataIntegrityViolationException?: not-null property references a null or transient value: dbnp.studycapturing.Sample.parentEvent; nested exception is org.hibernate.PropertyValueException?: not-null property references a null or transient value: dbnp.studycapturing.Sample.parentEvent, see log for stacktrace

This indicates a bug in the sample generation (you also see in the user interface that only the first sample listed actually has a parentEvent template name). This bug has to be fixed. But also, parentEvent should become an optional Sample property. Please change this and make sure the wizard still works.

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