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Annotator error messages unclear #3751

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fdlk opened this issue Sep 24, 2015 · 5 comments
Closed

Annotator error messages unclear #3751

fdlk opened this issue Sep 24, 2015 · 5 comments
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1.9 1.10 1.13 bug

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@fdlk
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fdlk commented Sep 24, 2015

When annotating the AnnotatorTest entity with negative POS attribute, I get the following error message:

Error! An error occurred. Please contact the administrator.
Message:For input string: ""

I'd expect a message that explains that the POS attribute is invalid plus an indication of which row is invalid.
@fdlk
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fdlk commented Sep 24, 2015

Server side stacktrace says

15:45:58.435 [ajp-bio-8009-exec-20] ERROR o.m.d.a.resources.impl.ResourcesImpl - Error querying Resource EXACTabixResource.
15:45:58.476 [ajp-bio-8009-exec-20] ERROR o.m.d.controller.AnnotatorController - -1
java.lang.ArrayIndexOutOfBoundsException: -1
    at org.molgenis.data.annotator.tabix.TabixReader.query(TabixReader.java:409) ~[molgenis-data-annotators-1.10.0-SNAPSHOT.jar:1.10.0-SNAPSHOT]
    at org.molgenis.data.annotator.tabix.TabixReader.query(TabixReader.java:464) ~[molgenis-data-annotators-1.10.0-SNAPSHOT.jar:1.10.0-SNAPSHOT]
    at org.molgenis.data.annotator.tabix.TabixVcfRepository.query(TabixVcfRepository.java:92) ~[molgenis-data-annotators-1.10.0-SNAPSHOT.jar:1.10.0-SNAPSHOT]
    at org.molgenis.data.annotator.tabix.TabixVcfRepository.findAll(TabixVcfRepository.java:75) ~[molgenis-data-annotators-1.10.0-SNAPSHOT.jar:1.10.0-SNAPSHOT]
    at org.molgenis.data.annotation.resources.impl.ResourceImpl.findAll(ResourceImpl.java:75) ~[molgenis-data-annotators-1.10.0-SNAPSHOT.jar:1.10.0-SNAPSHOT]
    at org.molgenis.data.annotation.resources.impl.ResourcesImpl.findAll(ResourcesImpl.java:50) ~[molgenis-data-annotators-1.10.0-SNAPSHOT.jar:1.10.0-SNAPSHOT]
    at org.molgenis.data.annotation.entity.impl.QueryAnnotatorImpl.annotateEntity(QueryAnnotatorImpl.java:89) ~[molgenis-data-annotators-1.10.0-SNAPSHOT.jar:1.10.0-SNAPSHOT]
    at org.molgenis.data.annotation.entity.impl.QueryAnnotatorImpl.annotateEntity(QueryAnnotatorImpl.java:31) ~[molgenis-data-annotators-1.10.0-SNAPSHOT.jar:1.10.0-SNAPSHOT]
    at org.molgenis.data.annotation.entity.impl.RepositoryAnnotatorImpl.annotateEntity(RepositoryAnnotatorImpl.java:53) ~[molgenis-data-annotators-1.10.0-SNAPSHOT.jar:1.10.0-SNAPSHOT]
    at org.molgenis.data.annotation.AbstractRepositoryEntityAnnotator$1.next(AbstractRepositoryEntityAnnotator.java:41) ~[molgenis-data-annotators-1.10.0-SNAPSHOT.jar:1.10.0-SNAPSHOT]
    at org.molgenis.data.annotation.AbstractRepositoryEntityAnnotator$1.next(AbstractRepositoryEntityAnnotator.java:18) ~[molgenis-data-annotators-1.10.0-SNAPSHOT.jar:1.10.0-SNAPSHOT]
    at org.molgenis.data.annotation.CrudRepositoryAnnotator.iterateOverEntitiesAndAnnotate(CrudRepositoryAnnotator.java:129) ~[molgenis-data-annotators-1.10.0-SNAPSHOT.jar:1.10.0-SNAPSHOT]
    at org.molgenis.data.annotation.CrudRepositoryAnnotator.lambda$annotate$4(CrudRepositoryAnnotator.java:109) ~[molgenis-data-annotators-1.10.0-SNAPSHOT.jar:1.10.0-SNAPSHOT]
    at org.molgenis.data.annotation.CrudRepositoryAnnotator$$Lambda$263/912397594.run(Unknown Source) ~[na:na]
    at org.molgenis.security.core.runas.RunAsSystemProxy.runAsSystem(RunAsSystemProxy.java:60) ~[molgenis-security-core-1.10.0-SNAPSHOT.jar:1.10.0-SNAPSHOT]
    at org.molgenis.data.annotation.CrudRepositoryAnnotator.annotate(CrudRepositoryAnnotator.java:95) ~[molgenis-data-annotators-1.10.0-SNAPSHOT.jar:1.10.0-SNAPSHOT]
    at org.molgenis.dataexplorer.controller.AnnotatorController.annotateData(AnnotatorController.java:128) ~[molgenis-dataexplorer-1.10.0-SNAPSHOT.jar:1.10.0-SNAPSHOT]
    at org.molgenis.dataexplorer.controller.AnnotatorController$$FastClassBySpringCGLIB$$30dc3d57.invoke(<generated>) ~[spring-core-4.1.6.RELEASE.jar:1.10.0-SNAPSHOT]
    at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:204) ~[spring-core-4.1.6.RELEASE.jar:4.1.6.RELEASE]
    at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:717) ~[spring-aop-4.1.6.RELEASE.jar:4.1.6.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) ~[spring-aop-4.1.6.RELEASE.jar:4.1.6.RELEASE]
    at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) ~[spring-tx-4.1.6.RELEASE.jar:4.1.6.RELEASE]
    at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281) ~[spring-tx-4.1.6.RELEASE.jar:4.1.6.RELEASE]
    at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) ~[spring-tx-4.1.6.RELEASE.jar:4.1.6.RELEASE]
    at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) ~[spring-aop-4.1.6.RELEASE.jar:4.1.6.RELEASE]
    at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:653) ~[spring-aop-4.1.6.RELEASE.jar:4.1.6.RELEASE]
    at org.molgenis.dataexplorer.controller.AnnotatorController$$EnhancerBySpringCGLIB$$d15eba67.annotateData(<generated>) ~[spring-core-4.1.6.RELEASE.jar:1.10.0-SNAPSHOT]
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.8.0_31]
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[na:1.8.0_31]
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.8.0_31]
    at java.lang.reflect.Method.invoke(Method.java:483) ~[na:1.8.0_31]
    at org.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:221) ~[spring-web-4.1.6.RELEASE.jar:4.1.6.RELEASE]
    at org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:137) ~[spring-web-4.1.6.RELEASE.jar:4.1.6.RELEASE]
    at org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:110) ~[spring-webmvc-4.1.6.RELEASE.jar:4.1.6.RELEASE]
    at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandleMethod(RequestMappingHandlerAdapter.java:776) ~[spring-webmvc-4.1.6.RELEASE.jar:4.1.6.RELEASE]
    at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:705) ~[spring-webmvc-4.1.6.RELEASE.jar:4.1.6.RELEASE]
    at org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:85) ~[spring-webmvc-4.1.6.RELEASE.jar:4.1.6.RELEASE]
    at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:959) ~[spring-webmvc-4.1.6.RELEASE.jar:4.1.6.RELEASE]
    at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:893) ~[spring-webmvc-4.1.6.RELEASE.jar:4.1.6.RELEASE]
    at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:966) [spring-webmvc-4.1.6.RELEASE.jar:4.1.6.RELEASE]
    at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:868) [spring-webmvc-4.1.6.RELEASE.jar:4.1.6.RELEASE]
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:646) [servlet-api.jar:na]
    at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:842) [spring-webmvc-4.1.6.RELEASE.jar:4.1.6.RELEASE]
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:727) [servlet-api.jar:na]
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303) [catalina.jar:7.0.59]
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) [catalina.jar:7.0.59]
    at org.springframework.web.filter.ShallowEtagHeaderFilter.doFilterInternal(ShallowEtagHeaderFilter.java:82) [spring-web-4.1.6.RELEASE.jar:4.1.6.RELEASE]
    at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) [spring-web-4.1.6.RELEASE.jar:4.1.6.RELEASE]
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) [catalina.jar:7.0.59]
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) [catalina.jar:7.0.59]
    at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52) [tomcat7-websocket.jar:7.0.59]
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) [catalina.jar:7.0.59]
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) [catalina.jar:7.0.59]
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:316) [spring-security-web-4.0.1.RELEASE.jar:4.0.1.RELEASE]
    at org.molgenis.security.MolgenisChangePasswordFilter.doFilter(MolgenisChangePasswordFilter.java:62) [molgenis-security-1.10.0-SNAPSHOT.jar:1.10.0-SNAPSHOT]
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) [spring-security-web-4.0.1.RELEASE.jar:4.0.1.RELEASE]
    at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:126) [spring-security-web-4.0.1.RELEASE.jar:4.0.1.RELEASE]
    at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:90) [spring-security-web-4.0.1.RELEASE.jar:4.0.1.RELEASE]
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) [spring-security-web-4.0.1.RELEASE.jar:4.0.1.RELEASE]
    at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:114) [spring-security-web-4.0.1.RELEASE.jar:4.0.1.RELEASE]
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) [spring-security-web-4.0.1.RELEASE.jar:4.0.1.RELEASE]
    at org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:122) [spring-security-web-4.0.1.RELEASE.jar:4.0.1.RELEASE]
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) [spring-security-web-4.0.1.RELEASE.jar:4.0.1.RELEASE]
    at org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:111) [spring-security-web-4.0.1.RELEASE.jar:4.0.1.RELEASE]
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) [spring-security-web-4.0.1.RELEASE.jar:4.0.1.RELEASE]
    at org.molgenis.security.MolgenisAnonymousAuthenticationFilter.doFilter(MolgenisAnonymousAuthenticationFilter.java:91) [molgenis-security-1.10.0-SNAPSHOT.jar:1.10.0-SNAPSHOT]
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) [spring-security-web-4.0.1.RELEASE.jar:4.0.1.RELEASE]
    at org.molgenis.security.token.TokenAuthenticationFilter.doFilter(TokenAuthenticationFilter.java:61) [molgenis-security-1.10.0-SNAPSHOT.jar:1.10.0-SNAPSHOT]
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) [spring-security-web-4.0.1.RELEASE.jar:4.0.1.RELEASE]
    at org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:168) [spring-security-web-4.0.1.RELEASE.jar:4.0.1.RELEASE]
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) [spring-security-web-4.0.1.RELEASE.jar:4.0.1.RELEASE]
    at org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:48) [spring-security-web-4.0.1.RELEASE.jar:4.0.1.RELEASE]
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) [spring-security-web-4.0.1.RELEASE.jar:4.0.1.RELEASE]
    at org.springframework.security.web.authentication.www.BasicAuthenticationFilter.doFilterInternal(BasicAuthenticationFilter.java:158) [spring-security-web-4.0.1.RELEASE.jar:4.0.1.RELEASE]
    at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) [spring-web-4.1.6.RELEASE.jar:4.1.6.RELEASE]
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) [spring-security-web-4.0.1.RELEASE.jar:4.0.1.RELEASE]
    at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:205) [spring-security-web-4.0.1.RELEASE.jar:4.0.1.RELEASE]
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) [spring-security-web-4.0.1.RELEASE.jar:4.0.1.RELEASE]
    at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:120) [spring-security-web-4.0.1.RELEASE.jar:4.0.1.RELEASE]
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) [spring-security-web-4.0.1.RELEASE.jar:4.0.1.RELEASE]
    at org.springframework.security.web.header.HeaderWriterFilter.doFilterInternal(HeaderWriterFilter.java:64) [spring-security-web-4.0.1.RELEASE.jar:4.0.1.RELEASE]
    at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) [spring-web-4.1.6.RELEASE.jar:4.1.6.RELEASE]
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) [spring-security-web-4.0.1.RELEASE.jar:4.0.1.RELEASE]
    at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:91) [spring-security-web-4.0.1.RELEASE.jar:4.0.1.RELEASE]
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) [spring-security-web-4.0.1.RELEASE.jar:4.0.1.RELEASE]
    at org.springframework.security.web.context.request.async.WebAsyncManagerIntegrationFilter.doFilterInternal(WebAsyncManagerIntegrationFilter.java:53) [spring-security-web-4.0.1.RELEASE.jar:4.0.1.RELEASE]
    at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) [spring-web-4.1.6.RELEASE.jar:4.1.6.RELEASE]
    at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) [spring-security-web-4.0.1.RELEASE.jar:4.0.1.RELEASE]
    at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:213) [spring-security-web-4.0.1.RELEASE.jar:4.0.1.RELEASE]
    at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:176) [spring-security-web-4.0.1.RELEASE.jar:4.0.1.RELEASE]
    at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:344) [spring-web-4.1.6.RELEASE.jar:4.1.6.RELEASE]
    at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:261) [spring-web-4.1.6.RELEASE.jar:4.1.6.RELEASE]
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) [catalina.jar:7.0.59]
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) [catalina.jar:7.0.59]
    at org.molgenis.ui.browserdetection.BrowserDetectionFilter.doFilter(BrowserDetectionFilter.java:56) [molgenis-core-ui-1.10.0-SNAPSHOT.jar:1.10.0-SNAPSHOT]
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) [catalina.jar:7.0.59]
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) [catalina.jar:7.0.59]
    at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220) [catalina.jar:7.0.59]
    at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122) [catalina.jar:7.0.59]
    at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:504) [catalina.jar:7.0.59]
    at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:170) [catalina.jar:7.0.59]
    at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103) [catalina.jar:7.0.59]
    at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:950) [catalina.jar:7.0.59]
    at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116) [catalina.jar:7.0.59]
    at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:421) [catalina.jar:7.0.59]
    at org.apache.coyote.ajp.AjpProcessor.process(AjpProcessor.java:190) [tomcat-coyote.jar:7.0.59]
    at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:611) [tomcat-coyote.jar:7.0.59]
    at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:314) [tomcat-coyote.jar:7.0.59]
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [na:1.8.0_31]
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [na:1.8.0_31]
    at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) [tomcat-coyote.jar:7.0.59]
    at java.lang.Thread.run(Thread.java:745) [na:1.8.0_31]

@fdlk fdlk changed the title Annotator error message unclear Exac annotator error message unclear Sep 24, 2015
@fdlk fdlk added the 1.10 label Sep 25, 2015
@fdlk fdlk modified the milestone: Sprint 73 Sep 28, 2015
@mark-de-haan mark-de-haan added this to the Sprint 73 milestone Sep 30, 2015
@bartcharbon bartcharbon self-assigned this Oct 1, 2015
@tommydeboer tommydeboer removed this from the Sprint 73 milestone Oct 1, 2015
@mark-de-haan mark-de-haan mentioned this issue Oct 1, 2015
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@tommydeboer tommydeboer added 1.9 and removed 1.10 labels Oct 1, 2015
@fdlk fdlk added 1.10 and removed 1.10.0-RC labels Oct 2, 2015
@bartcharbon
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The underlying error, which is described in a separate bug, is due to the chromosome of the entity is not present in the resource. This information might be helpful te reproduce this bug.

@mark-de-haan
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This should be fixed by #3853

@fdlk
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fdlk commented Oct 7, 2015

Well, yes and no. The bug will no longer occur and therefore the unclear error message will no longer be shown. But the test script demands that "A clear error message" should be shown in case of an error. Right now the message is simply copied from the exception but we should add some context. At the very least which of the checked annotators threw the exception, preferably also a clue as to which row was being annotated.

@fdlk fdlk added the 1.13.0-RC label Nov 17, 2015
@fdlk
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fdlk commented Nov 17, 2015

Still happens, but now if I enter a negative pos value. I've updated the description.

@fdlk fdlk changed the title Exac annotator error message unclear Annotator error messages unclear Nov 17, 2015
@bartcharbon bartcharbon removed their assignment Feb 2, 2016
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@mswertz @fdlk @dennishendriksen @mark-de-haan @bartcharbon @tommydeboer