Better error message when exporting a CAS with dangling relations as TSV

[lfoppiano]

Describe the bug
While exporting a project I received the following error:
Unexpected error during project export: ProjectExportException: Aborting due to unrecoverable error while exporting!

The log point to a NullPointerException:

Feb 15 10:19:14 falcon java[22160]: 2021-02-15 10:19:14 INFO [lfoppiano] LoggedEventExporter - Exported [5014] logged events for project [supercon-batch-7]
Feb 15 10:19:14 falcon java[22160]: 2021-02-15 10:19:14 INFO [lfoppiano] LoggedEventExporter - Skipped [1557] logged events for [230] documents no longer existing
Feb 15 10:19:14 falcon java[22160]: 2021-02-15 10:19:14 INFO [lfoppiano] LayerExporter - Exported [18] layers for project [supercon-batch-7]
Feb 15 10:19:14 falcon java[22160]: 2021-02-15 10:19:14 INFO [lfoppiano] PermissionsExporter - Exported [7] permissions for project [supercon-batch-7]
Feb 15 10:19:14 falcon java[22160]: 2021-02-15 10:19:14 INFO [lfoppiano] TagSetExporter - Exported [4] tagsets for project [supercon-batch-7]
Feb 15 10:19:14 falcon java[22160]: 2021-02-15 10:19:14 INFO [lfoppiano] SourceDocumentExporter - Exported content for source document [1020] in project [supercon-batch-7] with id [15]
Feb 15 10:19:14 falcon java[22160]: 2021-02-15 10:19:14 INFO [lfoppiano] SourceDocumentExporter - Exported content for source document [993] in project [supercon-batch-7] with id [15]
Feb 15 10:19:14 falcon java[22160]: 2021-02-15 10:19:14 INFO [lfoppiano] SourceDocumentExporter - Exported content for source document [1021] in project [supercon-batch-7] with id [15]
Feb 15 10:19:14 falcon java[22160]: 2021-02-15 10:19:14 INFO [lfoppiano] SourceDocumentExporter - Exported content for source document [1022] in project [supercon-batch-7] with id [15]
Feb 15 10:19:14 falcon java[22160]: 2021-02-15 10:19:14 INFO [lfoppiano] SourceDocumentExporter - Exported content for source document [1023] in project [supercon-batch-7] with id [15]
Feb 15 10:19:14 falcon java[22160]: 2021-02-15 10:19:14 INFO [lfoppiano] SourceDocumentExporter - Exported content for source document [998] in project [supercon-batch-7] with id [15]
Feb 15 10:19:14 falcon java[22160]: 2021-02-15 10:19:14 INFO [lfoppiano] SourceDocumentExporter - Exported content for source document [1024] in project [supercon-batch-7] with id [15]
Feb 15 10:19:14 falcon java[22160]: 2021-02-15 10:19:14 INFO [lfoppiano] SourceDocumentExporter - Exported content for source document [1000] in project [supercon-batch-7] with id [15]
Feb 15 10:19:14 falcon java[22160]: 2021-02-15 10:19:14 INFO [lfoppiano] SourceDocumentExporter - Exported content for source document [1025] in project [supercon-batch-7] with id [15]
Feb 15 10:19:14 falcon java[22160]: 2021-02-15 10:19:14 INFO [lfoppiano] SourceDocumentExporter - Exported content for source document [1026] in project [supercon-batch-7] with id [15]
Feb 15 10:19:14 falcon java[22160]: 2021-02-15 10:19:14 INFO [lfoppiano] SourceDocumentExporter - Exported content for source document [1027] in project [supercon-batch-7] with id [15]
Feb 15 10:19:14 falcon java[22160]: 2021-02-15 10:19:14 INFO [lfoppiano] SourceDocumentExporter - Exported content for source document [1045] in project [supercon-batch-7] with id [15]
Feb 15 10:19:14 falcon java[22160]: 2021-02-15 10:19:14 INFO [lfoppiano] SourceDocumentExporter - Exported content for source document [1029] in project [supercon-batch-7] with id [15]
Feb 15 10:19:14 falcon java[22160]: 2021-02-15 10:19:14 INFO [lfoppiano] SourceDocumentExporter - Exported content for source document [1030] in project [supercon-batch-7] with id [15]
Feb 15 10:19:14 falcon java[22160]: 2021-02-15 10:19:14 INFO [lfoppiano] SourceDocumentExporter - Exported content for source document [1031] in project [supercon-batch-7] with id [15]
Feb 15 10:19:14 falcon java[22160]: 2021-02-15 10:19:14 INFO [lfoppiano] SourceDocumentExporter - Exported content for source document [1032] in project [supercon-batch-7] with id [15]
Feb 15 10:19:14 falcon java[22160]: 2021-02-15 10:19:14 INFO [lfoppiano] SourceDocumentExporter - Exported content for source document [1033] in project [supercon-batch-7] with id [15]
Feb 15 10:19:14 falcon java[22160]: 2021-02-15 10:19:14 INFO [lfoppiano] SourceDocumentExporter - Exported content for source document [1034] in project [supercon-batch-7] with id [15]
Feb 15 10:19:14 falcon java[22160]: 2021-02-15 10:19:14 INFO [lfoppiano] SourceDocumentExporter - Exported content for source document [1035] in project [supercon-batch-7] with id [15]
Feb 15 10:19:14 falcon java[22160]: 2021-02-15 10:19:14 INFO [lfoppiano] SourceDocumentExporter - Exported content for source document [1036] in project [supercon-batch-7] with id [15]
Feb 15 10:19:14 falcon java[22160]: 2021-02-15 10:19:14 INFO [lfoppiano] SourceDocumentExporter - Exported content for source document [1037] in project [supercon-batch-7] with id [15]
Feb 15 10:19:14 falcon java[22160]: 2021-02-15 10:19:14 INFO [lfoppiano] SourceDocumentExporter - Exported content for source document [1038] in project [supercon-batch-7] with id [15]
Feb 15 10:19:14 falcon java[22160]: 2021-02-15 10:19:14 INFO [lfoppiano] SourceDocumentExporter - Exported content for source document [1039] in project [supercon-batch-7] with id [15]
Feb 15 10:19:14 falcon java[22160]: 2021-02-15 10:19:14 INFO [lfoppiano] SourceDocumentExporter - Exported content for source document [1040] in project [supercon-batch-7] with id [15]
Feb 15 10:19:14 falcon java[22160]: 2021-02-15 10:19:14 INFO [lfoppiano] SourceDocumentExporter - Exported content for source document [1041] in project [supercon-batch-7] with id [15]
Feb 15 10:19:14 falcon java[22160]: 2021-02-15 10:19:14 INFO [lfoppiano] SourceDocumentExporter - Exported content for source document [1042] in project [supercon-batch-7] with id [15]
Feb 15 10:19:14 falcon java[22160]: 2021-02-15 10:19:14 INFO [lfoppiano] SourceDocumentExporter - Exported content for source document [1043] in project [supercon-batch-7] with id [15]
Feb 15 10:19:14 falcon java[22160]: 2021-02-15 10:19:14 INFO [lfoppiano] ImportExportServiceImpl - Exported annotations [PR04310568-CC.superconductors.tsv](1020) for user [CURATION_USER] from project [supercon-batch-7](15) using format [ctsv3]
Feb 15 10:19:15 falcon java[22160]: 2021-02-15 10:19:15 INFO [lfoppiano] ImportExportServiceImpl - Exported annotations [PR0446999-CC.superconductors.tsv](993) for user [CURATION_USER] from project [supercon-batch-7](15) using format [ctsv3]
Feb 15 10:19:15 falcon java[22160]: 2021-02-15 10:19:15 INFO [lfoppiano] ImportExportServiceImpl - Exported annotations [PR04909084-CC.superconductors.tsv](1021) for user [CURATION_USER] from project [supercon-batch-7](15) using format [ctsv3]
Feb 15 10:19:15 falcon java[22160]: 2021-02-15 10:19:15 INFO [lfoppiano] ImportExportServiceImpl - Exported annotations [PR05003221-CC.superconductors.tsv](1022) for user [CURATION_USER] from project [supercon-batch-7](15) using format [ctsv3]
Feb 15 10:19:15 falcon java[22160]: 2021-02-15 10:19:15 INFO [lfoppiano] ImportExportServiceImpl - Exported annotations [PR05009672-CC.superconductors.tsv](1023) for user [CURATION_USER] from project [supercon-batch-7](15) using format [ctsv3]
Feb 15 10:19:15 falcon java[22160]: 2021-02-15 10:19:15 INFO [lfoppiano] ImportExportServiceImpl - Exported annotations [PR05511832-CC.superconductors.tsv](998) for user [CURATION_USER] from project [supercon-batch-7](15) using format [ctsv3]
Feb 15 10:19:15 falcon java[22160]: 2021-02-15 10:19:15 INFO [lfoppiano] ImportExportServiceImpl - Exported annotations [PR05514152-CC.superconductors.tsv](1024) for user [CURATION_USER] from project [supercon-batch-7](15) using format [ctsv3]
Feb 15 10:19:15 falcon java[22160]: 2021-02-15 10:19:15 INFO [lfoppiano] ImportExportServiceImpl - Exported annotations [PR05514733-CC.superconductors.tsv](1000) for user [CURATION_USER] from project [supercon-batch-7](15) using format [ctsv3]
Feb 15 10:19:15 falcon java[22160]: 2021-02-15 10:19:15 INFO [lfoppiano] ImportExportServiceImpl - Exported annotations [PR05703245-CC.superconductors.tsv](1025) for user [CURATION_USER] from project [supercon-batch-7](15) using format [ctsv3]
Feb 15 10:19:15 falcon java[22160]: 2021-02-15 10:19:15 INFO [lfoppiano] ImportExportServiceImpl - Exported annotations [PR05713422-CC.superconductors.tsv](1026) for user [CURATION_USER] from project [supercon-batch-7](15) using format [ctsv3]
Feb 15 10:19:15 falcon java[22160]: 2021-02-15 10:19:15 INFO [lfoppiano] ImportExportServiceImpl - Exported annotations [PR05809504-CC.superconductors.tsv](1027) for user [CURATION_USER] from project [supercon-batch-7](15) using format [ctsv3]
Feb 15 10:19:15 falcon java[22160]: 2021-02-15 10:19:15 INFO [lfoppiano] ImportExportServiceImpl - Exported annotations [PR05814581-CC.superconductors.tsv](1045) for user [CURATION_USER] from project [supercon-batch-7](15) using format [ctsv3]
Feb 15 10:19:15 falcon java[22160]: 2021-02-15 10:19:15 INFO [lfoppiano] ImportExportServiceImpl - Exported annotations [PR05814617-CC.superconductors.tsv](1029) for user [CURATION_USER] from project [supercon-batch-7](15) using format [ctsv3]
Feb 15 10:19:15 falcon java[22160]: 2021-02-15 10:19:15 INFO [lfoppiano] ImportExportServiceImpl - Exported annotations [PR05903948-CC.superconductors.tsv](1030) for user [CURATION_USER] from project [supercon-batch-7](15) using format [ctsv3]
Feb 15 10:19:15 falcon java[22160]: 2021-02-15 10:19:15 INFO [lfoppiano] ImportExportServiceImpl - Exported annotations [PR05907184-CC.superconductors.tsv](1031) for user [CURATION_USER] from project [supercon-batch-7](15) using format [ctsv3]
Feb 15 10:19:15 falcon java[22160]: 2021-02-15 10:19:15 ERROR [lfoppiano] PrimitiveAnalysisEngine_impl - Exception occurred
Feb 15 10:19:15 falcon java[22160]: org.apache.uima.analysis_engine.AnalysisEngineProcessException: Annotator processing failed.
Feb 15 10:19:15 falcon java[22160]: at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:406) [uimaj-core-3.1.1.jar!/:3.1.1]
Feb 15 10:19:15 falcon java[22160]: at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:299) [uimaj-core-3.1.1.jar!/:3.1.1]
Feb 15 10:19:15 falcon java[22160]: at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:272) [uimaj-core-3.1.1.jar!/:3.1.1]
Feb 15 10:19:15 falcon java[22160]: at de.tudarmstadt.ukp.clarin.webanno.api.dao.ImportExportServiceImpl.exportCasToFile(ImportExportServiceImpl.java:515) [webanno-api-dao-4.0.0-beta-22.jar!/:?]
Feb 15 10:19:15 falcon java[22160]: at de.tudarmstadt.ukp.clarin.webanno.api.dao.ImportExportServiceImpl.exportAnnotationDocument(ImportExportServiceImpl.java:251) [webanno-api-dao-4.0.0-beta-22.jar!/:?]
Feb 15 10:19:15 falcon java[22160]: at de.tudarmstadt.ukp.clarin.webanno.api.dao.ImportExportServiceImpl$$FastClassBySpringCGLIB$$256f1e29.invoke(<generated>) [webanno-api-dao-4.0.0-beta-22.jar!/:?]
Feb 15 10:19:15 falcon java[22160]: at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:218) [spring-core-5.3.3.jar!/:5.3.3]
Feb 15 10:19:15 falcon java[22160]: at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:779) [spring-aop-5.3.3.jar!/:5.3.3]
Feb 15 10:19:15 falcon java[22160]: at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) [spring-aop-5.3.3.jar!/:5.3.3]
Feb 15 10:19:15 falcon java[22160]: at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:750) [spring-aop-5.3.3.jar!/:5.3.3]
Feb 15 10:19:15 falcon java[22160]: at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:123) [spring-tx-5.3.3.jar!/:5.3.3]
Feb 15 10:19:15 falcon java[22160]: at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:388) [spring-tx-5.3.3.jar!/:5.3.3]
Feb 15 10:19:15 falcon java[22160]: at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:119) [spring-tx-5.3.3.jar!/:5.3.3]
Feb 15 10:19:15 falcon java[22160]: at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) [spring-aop-5.3.3.jar!/:5.3.3]
Feb 15 10:19:15 falcon java[22160]: at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:750) [spring-aop-5.3.3.jar!/:5.3.3]
Feb 15 10:19:15 falcon java[22160]: at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:692) [spring-aop-5.3.3.jar!/:5.3.3]
Feb 15 10:19:15 falcon java[22160]: at de.tudarmstadt.ukp.clarin.webanno.api.dao.ImportExportServiceImpl$$EnhancerBySpringCGLIB$$906905fd.exportAnnotationDocument(<generated>) [webanno-api-dao-4.0.0-beta-22.jar!/:?]
Feb 15 10:19:15 falcon java[22160]: at de.tudarmstadt.ukp.clarin.webanno.api.dao.export.exporters.CuratedDocumentsExporter.exportData(CuratedDocumentsExporter.java:145) [webanno-api-dao-4.0.0-beta-22.jar!/:?]
Feb 15 10:19:15 falcon java[22160]: at de.tudarmstadt.ukp.clarin.webanno.api.dao.export.ProjectExportServiceImpl.exportProject(ProjectExportServiceImpl.java:224) [webanno-api-dao-4.0.0-beta-22.jar!/:?]
Feb 15 10:19:15 falcon java[22160]: at de.tudarmstadt.ukp.clarin.webanno.api.dao.export.ProjectExportServiceImpl.exportProject(ProjectExportServiceImpl.java:168) [webanno-api-dao-4.0.0-beta-22.jar!/:?]
Feb 15 10:19:15 falcon java[22160]: at de.tudarmstadt.ukp.clarin.webanno.api.dao.export.ProjectExportServiceImpl$$FastClassBySpringCGLIB$$3d43e16f.invoke(<generated>) [webanno-api-dao-4.0.0-beta-22.jar!/:?]
Feb 15 10:19:15 falcon java[22160]: at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:218) [spring-core-5.3.3.jar!/:5.3.3]
Feb 15 10:19:15 falcon java[22160]: at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:779) [spring-aop-5.3.3.jar!/:5.3.3]
Feb 15 10:19:15 falcon java[22160]: at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) [spring-aop-5.3.3.jar!/:5.3.3]
Feb 15 10:19:15 falcon java[22160]: at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:750) [spring-aop-5.3.3.jar!/:5.3.3]
Feb 15 10:19:15 falcon java[22160]: at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:123) [spring-tx-5.3.3.jar!/:5.3.3]
Feb 15 10:19:15 falcon java[22160]: at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:388) [spring-tx-5.3.3.jar!/:5.3.3]
Feb 15 10:19:15 falcon java[22160]: at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:119) [spring-tx-5.3.3.jar!/:5.3.3]
Feb 15 10:19:15 falcon java[22160]: at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) [spring-aop-5.3.3.jar!/:5.3.3]
Feb 15 10:19:15 falcon java[22160]: at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:750) [spring-aop-5.3.3.jar!/:5.3.3]
Feb 15 10:19:15 falcon java[22160]: at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:692) [spring-aop-5.3.3.jar!/:5.3.3]
Feb 15 10:19:15 falcon java[22160]: at de.tudarmstadt.ukp.clarin.webanno.api.dao.export.ProjectExportServiceImpl$$EnhancerBySpringCGLIB$$32008b8f.exportProject(<generated>) [webanno-api-dao-4.0.0-beta-22.jar!/:?]
Feb 15 10:19:15 falcon java[22160]: at de.tudarmstadt.ukp.clarin.webanno.api.dao.export.ProjectExportFullProjectTask.export(ProjectExportFullProjectTask.java:46) [webanno-api-dao-4.0.0-beta-22.jar!/:?]
Feb 15 10:19:15 falcon java[22160]: at de.tudarmstadt.ukp.clarin.webanno.api.dao.export.ProjectExportTask_ImplBase.run(ProjectExportTask_ImplBase.java:79) [webanno-api-dao-4.0.0-beta-22.jar!/:?]
Feb 15 10:19:15 falcon java[22160]: at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) [?:?]
Feb 15 10:19:15 falcon java[22160]: at java.util.concurrent.FutureTask.run(FutureTask.java:264) [?:?]
Feb 15 10:19:15 falcon java[22160]: at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) [?:?]
Feb 15 10:19:15 falcon java[22160]: at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) [?:?]
Feb 15 10:19:15 falcon java[22160]: at java.lang.Thread.run(Thread.java:834) [?:?]
Feb 15 10:19:15 falcon java[22160]: Caused by: java.lang.NullPointerException
Feb 15 10:19:15 falcon java[22160]: at de.tudarmstadt.ukp.clarin.webanno.tsv.internal.tsv3x.Tsv3XSerializer.writeRelationReference(Tsv3XSerializer.java:320) ~[webanno-io-tsv-4.0.0-beta-22.jar!/:?]
Feb 15 10:19:15 falcon java[22160]: at de.tudarmstadt.ukp.clarin.webanno.tsv.internal.tsv3x.Tsv3XSerializer.writeValue(Tsv3XSerializer.java:267) ~[webanno-io-tsv-4.0.0-beta-22.jar!/:?]
Feb 15 10:19:15 falcon java[22160]: at de.tudarmstadt.ukp.clarin.webanno.tsv.internal.tsv3x.Tsv3XSerializer.writeValues(Tsv3XSerializer.java:246) ~[webanno-io-tsv-4.0.0-beta-22.jar!/:?]
Feb 15 10:19:15 falcon java[22160]: at de.tudarmstadt.ukp.clarin.webanno.tsv.internal.tsv3x.Tsv3XSerializer.write(Tsv3XSerializer.java:226) ~[webanno-io-tsv-4.0.0-beta-22.jar!/:?]
Feb 15 10:19:15 falcon java[22160]: at de.tudarmstadt.ukp.clarin.webanno.tsv.internal.tsv3x.Tsv3XSerializer.write(Tsv3XSerializer.java:198) ~[webanno-io-tsv-4.0.0-beta-22.jar!/:?]
Feb 15 10:19:15 falcon java[22160]: at de.tudarmstadt.ukp.clarin.webanno.tsv.internal.tsv3x.Tsv3XSerializer.write(Tsv3XSerializer.java:79) ~[webanno-io-tsv-4.0.0-beta-22.jar!/:?]
Feb 15 10:19:15 falcon java[22160]: at de.tudarmstadt.ukp.clarin.webanno.tsv.WebannoTsv3XWriter.process(WebannoTsv3XWriter.java:67) ~[webanno-io-tsv-4.0.0-beta-22.jar!/:?]
Feb 15 10:19:15 falcon java[22160]: at org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCasAnnotator_ImplBase.java:48) ~[uimaj-core-3.1.1.jar!/:3.1.1]
Feb 15 10:19:15 falcon java[22160]: at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.lambda$callProcessMethod$3(AnalysisEngineImplBase.java:626) ~[uimaj-core-3.1.1.jar!/:3.1.1]
Feb 15 10:19:15 falcon java[22160]: at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.withContexts(AnalysisEngineImplBase.java:643) ~[uimaj-core-3.1.1.jar!/:3.1.1]
Feb 15 10:19:15 falcon java[22160]: at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.callProcessMethod(AnalysisEngineImplBase.java:623) ~[uimaj-core-3.1.1.jar!/:3.1.1]
Feb 15 10:19:15 falcon java[22160]: at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:381) ~[uimaj-core-3.1.1.jar!/:3.1.1]
Feb 15 10:19:15 falcon java[22160]: ... 38 more
Feb 15 10:19:15 falcon java[22160]: 2021-02-15 10:19:15 ERROR [lfoppiano] ProjectExportFullProjectTask - Unexpected error during project export
Feb 15 10:19:15 falcon java[22160]: de.tudarmstadt.ukp.clarin.webanno.api.export.ProjectExportException: Project export failed
Feb 15 10:19:15 falcon java[22160]: at de.tudarmstadt.ukp.clarin.webanno.api.dao.export.ProjectExportServiceImpl.exportProject(ProjectExportServiceImpl.java:243) ~[webanno-api-dao-4.0.0-beta-22.jar!/:?]
Feb 15 10:19:15 falcon java[22160]: at de.tudarmstadt.ukp.clarin.webanno.api.dao.export.ProjectExportServiceImpl.exportProject(ProjectExportServiceImpl.java:168) ~[webanno-api-dao-4.0.0-beta-22.jar!/:?]
Feb 15 10:19:15 falcon java[22160]: at de.tudarmstadt.ukp.clarin.webanno.api.dao.export.ProjectExportServiceImpl$$FastClassBySpringCGLIB$$3d43e16f.invoke(<generated>) ~[webanno-api-dao-4.0.0-beta-22.jar!/:?]
Feb 15 10:19:15 falcon java[22160]: at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:218) ~[spring-core-5.3.3.jar!/:5.3.3]
Feb 15 10:19:15 falcon java[22160]: at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:779) ~[spring-aop-5.3.3.jar!/:5.3.3]
Feb 15 10:19:15 falcon java[22160]: at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163) ~[spring-aop-5.3.3.jar!/:5.3.3]
Feb 15 10:19:15 falcon java[22160]: at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:750) ~[spring-aop-5.3.3.jar!/:5.3.3]
Feb 15 10:19:15 falcon java[22160]: at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:123) ~[spring-tx-5.3.3.jar!/:5.3.3]
Feb 15 10:19:15 falcon java[22160]: at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:388) ~[spring-tx-5.3.3.jar!/:5.3.3]
Feb 15 10:19:15 falcon java[22160]: at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:119) ~[spring-tx-5.3.3.jar!/:5.3.3]
Feb 15 10:19:15 falcon java[22160]: at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186) ~[spring-aop-5.3.3.jar!/:5.3.3]
Feb 15 10:19:15 falcon java[22160]: at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.proceed(CglibAopProxy.java:750) ~[spring-aop-5.3.3.jar!/:5.3.3]
Feb 15 10:19:15 falcon java[22160]: at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:692) ~[spring-aop-5.3.3.jar!/:5.3.3]
Feb 15 10:19:15 falcon java[22160]: at de.tudarmstadt.ukp.clarin.webanno.api.dao.export.ProjectExportServiceImpl$$EnhancerBySpringCGLIB$$32008b8f.exportProject(<generated>) ~[webanno-api-dao-4.0.0-beta-22.jar!/:?]
Feb 15 10:19:15 falcon java[22160]: at de.tudarmstadt.ukp.clarin.webanno.api.dao.export.ProjectExportFullProjectTask.export(ProjectExportFullProjectTask.java:46) ~[webanno-api-dao-4.0.0-beta-22.jar!/:?]
Feb 15 10:19:15 falcon java[22160]: at de.tudarmstadt.ukp.clarin.webanno.api.dao.export.ProjectExportTask_ImplBase.run(ProjectExportTask_ImplBase.java:79) [webanno-api-dao-4.0.0-beta-22.jar!/:?]
Feb 15 10:19:15 falcon java[22160]: at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515) [?:?]
Feb 15 10:19:15 falcon java[22160]: at java.util.concurrent.FutureTask.run(FutureTask.java:264) [?:?]
Feb 15 10:19:15 falcon java[22160]: at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) [?:?]
Feb 15 10:19:15 falcon java[22160]: at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) [?:?]
Feb 15 10:19:15 falcon java[22160]: at java.lang.Thread.run(Thread.java:834) [?:?]
Feb 15 10:19:15 falcon java[22160]: Caused by: de.tudarmstadt.ukp.clarin.webanno.api.export.ProjectExportException: Aborting due to unrecoverable error while exporting!
Feb 15 10:19:15 falcon java[22160]: at de.tudarmstadt.ukp.clarin.webanno.api.dao.export.exporters.CuratedDocumentsExporter.exportData(CuratedDocumentsExporter.java:154) ~[webanno-api-dao-4.0.0-beta-22.jar!/:?]
Feb 15 10:19:15 falcon java[22160]: at de.tudarmstadt.ukp.clarin.webanno.api.dao.export.ProjectExportServiceImpl.exportProject(ProjectExportServiceImpl.java:224) ~[webanno-api-dao-4.0.0-beta-22.jar!/:?]
Feb 15 10:19:15 falcon java[22160]: ... 20 more
Feb 15 10:19:16 falcon java[22160]: 2021-02-15 10:19:16 ERROR [lfoppiano] ApplicationPageBase - lfoppiano: Unexpected error during project export: ProjectExportException: Aborting due to unrecoverable error while exporting!
Feb 15 10:19:16 falcon java[22160]: 2021-02-15 10:19:16 ERROR [lfoppiano] ApplicationPageBase - lfoppiano: Project export failed

This issue occurs only with TSV export.

To Reproduce
I'm not sure how to provide you the data for reproduce it

Expected behaviour
Maybe export what can be exported and ignore the rest?

Please complete the following information:

• Version and build ID: 0.18.1 (2021-02-10 23:33:09, build d108e4b)
• OS: Linux
• Browser: Chrome / Firefox

[reckart]

Looking at the code that throws the exception, I would say that there is a relation that has dangling endpoints.

Please try running the CAS Doctor over the project. It should report this type of inconsistency and there should be a repair action that you can perform. It is a good idea to create a backup of the project (export as XMI or binary CAS) before applying CAS Doctor repairs.

[reckart]

There is an option to activate the CAS doctor on every single load and save action to fail immediately if an action is about to cause an inconsistency or to immediately detect inconsistent files when opening them - but it may significantly slow down the application.

If you want to try, you could add this option to your settings.properties file:

debug.casDoctor.checks=AllFeatureStructuresIndexedCheck

[lfoppiano]

Thanks @reckart, after exporting a backup of the project, I ran the check CasDoctor and indeed there is some sort of problem:

PR05909642-CC.superconductors.tsv [CURATION_USER]
--
ERROR | AllFeatureStructuresIndexedCheck | Unindexed feature structures: 2
ERROR | AllFeatureStructuresIndexedCheck | Non-indexed feature structure [Supercon:70125    sofa: _InitialView    begin: 4735    end: 4739    extra_tag: <null>    supercon_tag: "tcValue"] reachable through [Supercon_link:70575    sofa: _InitialView    begin: 4782    end: 4794    Dependent: Supercon:70131       sofa: _InitialView       begin: 4782       end: 4794       extra_tag: <null>       supercon_tag: "material"    Governor: Supercon:70125       sofa: _InitialView       begin: 4735       end: 4739       extra_tag: <null>       supercon_tag: "tcValue"    relationships: "tcValue-material"]
ERROR | AllFeatureStructuresIndexedCheck | Non-indexed feature structure [Supercon:70131    sofa: _InitialView    begin: 4782    end: 4794    extra_tag: <null>    supercon_tag: "material"] reachable through [Supercon_link:70575    sofa: _InitialView    begin: 4782    end: 4794    Dependent: Supercon:70131       sofa: _InitialView       begin: 4782       end: 4794       extra_tag: <null>       supercon_tag: "material"    Governor: Supercon:70125       sofa: _InitialView       begin: 4735       end: 4739       extra_tag: <null>       supercon_tag: "tcValue"    relationships: "tcValue-material"]

but then when I try to fix it, I get:

PR05909642-CC.superconductors.tsv [CURATION_USER]
--
ERROR | ProjectCasDoctorPanel | Error checking annotations for [CURATION_USER] for  [PR05909642-CC.superconductors.tsv]: Repair attempt failed - ask system  administrator for details.

I tried to locate the exception in the log file, but I'm not sure I'm reporting the right part, as the exception is very long. It seems WriteAccess exception, although the document has been unlocked from the curation part.

I think I will not enable the check as it might slow down the application user experience

[reckart]

Problem reported with the CAS doctor repair action may be a duplicate of #1788.

[lfoppiano]

ah I see. I would go around this by removing the document.

[reckart]

I would love to debug and fix this - unfortunately, I haven't been able yet to reproduce it locally...

[lfoppiano]

@reckart no problem, I can share you the project. I left in just the problematic file..

copy_of_supercon-batch-7_project_2021-02-17_0915.zip

Let me know if it's enough

[reckart]

We hopefully have a fix restoring the ability to repair CASes and hopefully not breaking anything else incoming here: #2005

[reckart]

Would be cool if we could figure out why the dangling relation turned up in the first place though...

[lfoppiano]

I'm going to try to find out, although I doubt non-technical people know what they are doing when they annotate ;-)

[lfoppiano]

I've been going through the log and I've seen two main things:

1. concurrent modification errors while annotating (although the annotation version of the document is fine), although after that I had exported the project for backup and it worked.
2. no exception when the curator was working on this document, see log below:

Feb 09 10:20:45 falcon java[19336]: 2021-02-09 10:20:45 INFO [pedro] AnnotationSchemaServiceImpl - Upgraded CAS of user [CURATION_USER] for document [PR05909642-CC.superconductors.tsv](1032) in project [supercon-batch-7](15)
Feb 09 10:21:01 falcon java[19336]: 2021-02-09 10:21:01 INFO [pedro] ApplicationPageBase - pedro: The [supercon] annotation has been deleted.
Feb 09 10:22:27 falcon java[19336]: 2021-02-09 10:22:27 INFO [pedro] ApplicationPageBase - pedro: The attached annotation for relation type [supercon_link] has been deleted
Feb 09 10:22:27 falcon java[19336]: 2021-02-09 10:22:27 INFO [pedro] ApplicationPageBase - pedro: The [supercon] annotation has been deleted.
Feb 09 10:43:51 falcon java[19336]: 2021-02-09 10:43:51 INFO [pedro] ApplicationPageBase - pedro: The [supercon] annotation has been deleted.
Feb 09 10:50:50 falcon java[19336]: 2021-02-09 10:50:50 INFO [pedro] ApplicationPageBase - pedro: The [supercon] annotation has been deleted.
Feb 09 10:55:03 falcon java[19336]: 2021-02-09 10:55:03 INFO [pedro] ApplicationPageBase - pedro: The [supercon] annotation has been deleted.
Feb 09 10:55:07 falcon java[19336]: 2021-02-09 10:55:07 INFO [pedro] ApplicationPageBase - pedro: The [supercon] annotation has been deleted.
Feb 09 11:11:57 falcon java[19336]: 2021-02-09 11:11:57 INFO [pedro] ApplicationPageBase - pedro: The [supercon] annotation has been deleted.
Feb 09 11:20:50 falcon java[19336]: 2021-02-09 11:20:50 INFO [pedro] ApplicationPageBase - pedro: The [supercon] annotation has been deleted.
Feb 09 11:20:59 falcon java[19336]: 2021-02-09 11:20:59 INFO [pedro] ApplicationPageBase - pedro: The [supercon] annotation has been deleted.
Feb 09 11:43:53 falcon java[19336]: 2021-02-09 11:43:53 INFO [pedro] ApplicationPageBase - pedro: The [supercon_link] annotation has been deleted.

Not sure if this can help much

[reckart]

The saving of all annotations on a document happens atomically - kind of like in a transaction. So if there are two people saving concurrently, one wins with all their annotation and the other one loses and gets the concurrent modification error (if that is the kind of concurrent modification exception from the CAS storage we are talking about).

However, you could try adding -Dwebanno.debug.enforce_cas_thread_lock=true while starting the server which installs an extra safeguard to check that no two threads are trying to concurrently access the CAS. If such an access would be detected, the safeguard generates an error. This is something we tend to have enabled while developing to detect any potential concurrent accesses, but it is not enabled by default. There is no significant performance overhead.

The most probably cause for a dangling relation is that while deleting a span, the application did not discover all relations that connect to this span. Might be a classic case for implementing a (randomizing) test-case...