java.lang.NullPointerException: Cannot invoke "org.eclipse.persistence.descriptors.DescriptorEvent.getDescriptor()" because "event" is null
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Type: Bug
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Description
I'm on 9ce5dd1 (latest in develop) and the script I'm testing https://github.com/gdcc/dataverse-recipes/pull/3 created 90 out of 95 datasets it was trying to create but then exited, showing a 500 error from Dataverse. I'm not sure what's going on.
(venv) pdurbin@beamish create-datasets-from-excel % python create-datasets-from-excel.py
๐ Connected to 'http://localhost:8080/'
Dataset with pid 'doi:10.5072/FK2/CHNSWY' created.
Title: Soil Climate Analysis Network (SCAN)
Description: SCAN monitors soil moisture, soil temperature, precipitation, air temperature, and other variables critical for agricultural decision-making.
Agency Responsible: USDA Natural Resources Conservation Service (NRCS)
Access Link Name: SCAN Data and Products
Access Link URL: https://www.nrcs.usda.gov/resources/data-and-reports/soil-climate-analysis-network
Fetching dataset 'doi:10.5072/FK2/CHNSWY' from 'http://localhost:8080/'
โญโโ Dataset Information โโโฎ
โ Title: Darwin's Finches โ
โ Version: latest โ
โ Files: 0 โ
โฐโโโโโโโโโโโโโโโโโโโโโโโโโโฏ
Dataset with pid 'doi:10.5072/FK2/FPTFNB' created.
[snip]
Title: Farm Labor Markets in the United States and Mexico
Description: This report examines the dynamics of farm labor markets, focusing on the supply of farm labor from Mexico and its implications for U.S. agriculture.
Agency Responsible: USDA Economic Research Service (ERS)
Access Link Name: Farm Labor Markets Report
Access Link URL: https://www.ers.usda.gov/publications/pub-details/?pubid=90831
Fetching dataset 'doi:10.5072/FK2/ZRZ4D5' from 'http://localhost:8080/'
โญโโ Dataset Information โโโฎ
โ Title: Darwin's Finches โ
โ Version: latest โ
โ Files: 0 โ
โฐโโโโโโโโโโโโโโโโโโโโโโโโโโฏ
Traceback (most recent call last):
File "/Users/PDurbin/github/gdcc/dataverse-recipes/python/create-datasets-from-excel/create-datasets-from-excel.py", line 143, in <module>
dataset.update()
File "/Users/PDurbin/github/gdcc/dataverse-recipes/python/create-datasets-from-excel/venv/lib/python3.12/site-packages/easyDataverse/dataset.py", line 237, in update
update_dataset(
File "/Users/PDurbin/github/gdcc/dataverse-recipes/python/create-datasets-from-excel/venv/lib/python3.12/site-packages/easyDataverse/uploader.py", line 121, in update_dataset
_update_metadata(
File "/Users/PDurbin/github/gdcc/dataverse-recipes/python/create-datasets-from-excel/venv/lib/python3.12/site-packages/easyDataverse/uploader.py", line 159, in _update_metadata
response.raise_for_status()
File "/Users/PDurbin/github/gdcc/dataverse-recipes/python/create-datasets-from-excel/venv/lib/python3.12/site-packages/requests/models.py", line 1024, in raise_for_status
raise HTTPError(http_error_msg, response=self)
requests.exceptions.HTTPError: 500 Server Error: Internal Server Error for url: http://localhost:8080/api/datasets/:persistentId/editMetadata?persistentId=doi:10.5072/FK2/ZRZ4D5&replace=true
(venv) pdurbin@beamish create-datasets-from-excel %
Stacktrace:
dev_dataverse> [#|2025-02-27T14:38:30.524+0000|WARNING|Payara 6.2024.6|org.eclipse.persistence.session./file:/opt/payara/deployments/dataverse/WEB-INF/classes/_VDCNet-ejbPU|_ThreadID=315;_ThreadName=__ejb-thread-pool15;_TimeMillis=1740667110524;_LevelValue=900;|
dev_dataverse> java.lang.NullPointerException: Cannot invoke "org.eclipse.persistence.descriptors.DescriptorEvent.getDescriptor()" because "event" is null
dev_dataverse> at org.eclipse.persistence.internal.sessions.AbstractSession.executeDeferredEvents(AbstractSession.java:1479)
dev_dataverse> at org.eclipse.persistence.internal.sessions.UnitOfWorkImpl.internalExecuteQuery(UnitOfWorkImpl.java:3009)
dev_dataverse> at org.eclipse.persistence.internal.sessions.AbstractSession.executeQuery(AbstractSession.java:1841)
dev_dataverse> at org.eclipse.persistence.internal.sessions.AbstractSession.executeQuery(AbstractSession.java:1823)
dev_dataverse> at org.eclipse.persistence.internal.indirection.NoIndirectionPolicy.valueFromQuery(NoIndirectionPolicy.java:352)
dev_dataverse> at org.eclipse.persistence.mappings.ForeignReferenceMapping.valueFromRowInternal(ForeignReferenceMapping.java:2343)
dev_dataverse> at org.eclipse.persistence.mappings.OneToOneMapping.valueFromRowInternal(OneToOneMapping.java:1874)
dev_dataverse> at org.eclipse.persistence.mappings.ForeignReferenceMapping.valueFromRow(ForeignReferenceMapping.java:2184)
dev_dataverse> at org.eclipse.persistence.mappings.ForeignReferenceMapping.buildCloneFromRow(ForeignReferenceMapping.java:341)
dev_dataverse> at org.eclipse.persistence.internal.descriptors.ObjectBuilder.buildAttributesIntoWorkingCopyClone(ObjectBuilder.java:2111)
dev_dataverse> at org.eclipse.persistence.internal.descriptors.ObjectBuilder.buildWorkingCopyCloneFromRow(ObjectBuilder.java:2364)
dev_dataverse> at org.eclipse.persistence.internal.descriptors.ObjectBuilder.buildObjectInUnitOfWork(ObjectBuilder.java:958)
dev_dataverse> at org.eclipse.persistence.internal.descriptors.ObjectBuilder.buildObjectInternal(ObjectBuilder.java:844)
dev_dataverse> at org.eclipse.persistence.internal.descriptors.ObjectBuilder.buildObject(ObjectBuilder.java:799)
dev_dataverse> at org.eclipse.persistence.internal.descriptors.ObjectBuilder.buildObject(ObjectBuilder.java:777)
dev_dataverse> at org.eclipse.persistence.queries.ObjectLevelReadQuery.buildObject(ObjectLevelReadQuery.java:863)
dev_dataverse> at org.eclipse.persistence.queries.ReadAllQuery.registerResultInUnitOfWork(ReadAllQuery.java:987)
dev_dataverse> at org.eclipse.persistence.queries.ReadAllQuery.executeObjectLevelReadQuery(ReadAllQuery.java:598)
dev_dataverse> at org.eclipse.persistence.queries.ObjectLevelReadQuery.executeDatabaseQuery(ObjectLevelReadQuery.java:1236)
dev_dataverse> at org.eclipse.persistence.queries.DatabaseQuery.execute(DatabaseQuery.java:913)
dev_dataverse> at org.eclipse.persistence.queries.ObjectLevelReadQuery.execute(ObjectLevelReadQuery.java:1195)
dev_dataverse> at org.eclipse.persistence.queries.ReadAllQuery.execute(ReadAllQuery.java:485)
dev_dataverse> at org.eclipse.persistence.queries.ObjectLevelReadQuery.executeInUnitOfWork(ObjectLevelReadQuery.java:1283)
dev_dataverse> at org.eclipse.persistence.internal.sessions.UnitOfWorkImpl.internalExecuteQuery(UnitOfWorkImpl.java:3008)
dev_dataverse> at org.eclipse.persistence.internal.sessions.AbstractSession.executeQuery(AbstractSession.java:1841)
dev_dataverse> at org.eclipse.persistence.internal.sessions.AbstractSession.executeQuery(AbstractSession.java:1823)
dev_dataverse> at org.eclipse.persistence.internal.indirection.QueryBasedValueHolder.instantiate(QueryBasedValueHolder.java:136)
dev_dataverse> at org.eclipse.persistence.internal.indirection.QueryBasedValueHolder.instantiate(QueryBasedValueHolder.java:122)
dev_dataverse> at org.eclipse.persistence.internal.indirection.DatabaseValueHolder.getValue(DatabaseValueHolder.java:103)
dev_dataverse> at org.eclipse.persistence.internal.indirection.UnitOfWorkValueHolder.instantiateImpl(UnitOfWorkValueHolder.java:176)
dev_dataverse> at org.eclipse.persistence.internal.indirection.UnitOfWorkValueHolder.instantiate(UnitOfWorkValueHolder.java:244)
dev_dataverse> at org.eclipse.persistence.internal.indirection.DatabaseValueHolder.getValue(DatabaseValueHolder.java:103)
dev_dataverse> at org.eclipse.persistence.indirection.IndirectList.buildDelegate(IndirectList.java:275)
dev_dataverse> at org.eclipse.persistence.indirection.IndirectList.getDelegate(IndirectList.java:458)
dev_dataverse> at org.eclipse.persistence.indirection.IndirectList$1.<init>(IndirectList.java:602)
dev_dataverse> at org.eclipse.persistence.indirection.IndirectList.listIterator(IndirectList.java:601)
dev_dataverse> at org.eclipse.persistence.indirection.IndirectList.iterator(IndirectList.java:560)
dev_dataverse> at edu.harvard.iq.dataverse.DatasetVersion.initDatasetFields(DatasetVersion.java:1626)
dev_dataverse> at edu.harvard.iq.dataverse.DatasetVersion.isValid(DatasetVersion.java:1759)
dev_dataverse> at edu.harvard.iq.dataverse.search.IndexServiceBean.toSolrDocs(IndexServiceBean.java:939)
dev_dataverse> at edu.harvard.iq.dataverse.search.IndexServiceBean.addOrUpdateDataset(IndexServiceBean.java:1748)
dev_dataverse> at edu.harvard.iq.dataverse.search.IndexServiceBean.addOrUpdateDataset(IndexServiceBean.java:920)
dev_dataverse> at edu.harvard.iq.dataverse.search.IndexServiceBean.doIndexDataset(IndexServiceBean.java:653)
dev_dataverse> at edu.harvard.iq.dataverse.search.IndexServiceBean.indexDataset(IndexServiceBean.java:474)
dev_dataverse> at edu.harvard.iq.dataverse.search.IndexServiceBean.doAsyncIndexDataset(IndexServiceBean.java:439)
dev_dataverse> at edu.harvard.iq.dataverse.search.IndexServiceBean.asyncIndexDataset(IndexServiceBean.java:423)
dev_dataverse> at jdk.internal.reflect.GeneratedMethodAccessor454.invoke(Unknown Source)
dev_dataverse> at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
dev_dataverse> at java.base/java.lang.reflect.Method.invoke(Unknown Source)
dev_dataverse> at org.glassfish.ejb.security.application.EJBSecurityManager.runMethod(EJBSecurityManager.java:588)
dev_dataverse> at org.glassfish.ejb.security.application.EJBSecurityManager.invoke(EJBSecurityManager.java:408)
dev_dataverse> at com.sun.ejb.containers.BaseContainer.invokeBeanMethod(BaseContainer.java:4835)
dev_dataverse> at com.sun.ejb.EjbInvocation.invokeBeanMethod(EjbInvocation.java:653)
dev_dataverse> at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:834)
dev_dataverse> at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:603)
dev_dataverse> at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.doCall(SystemInterceptorProxy.java:163)
dev_dataverse> at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.aroundInvoke(SystemInterceptorProxy.java:140)
dev_dataverse> at jdk.internal.reflect.GeneratedMethodAccessor191.invoke(Unknown Source)
dev_dataverse> at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
dev_dataverse> at java.base/java.lang.reflect.Method.invoke(Unknown Source)
dev_dataverse> at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:888)
dev_dataverse> at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:833)
dev_dataverse> at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:603)
dev_dataverse> at org.jboss.weld.module.ejb.AbstractEJBRequestScopeActivationInterceptor.aroundInvoke(AbstractEJBRequestScopeActivationInterceptor.java:81)
dev_dataverse> at org.jboss.weld.module.ejb.SessionBeanInterceptor.aroundInvoke(SessionBeanInterceptor.java:52)
dev_dataverse> at jdk.internal.reflect.GeneratedMethodAccessor171.invoke(Unknown Source)
dev_dataverse> at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
dev_dataverse> at java.base/java.lang.reflect.Method.invoke(Unknown Source)
dev_dataverse> at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:888)
dev_dataverse> at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:833)
dev_dataverse> at com.sun.ejb.containers.interceptors.InterceptorManager.intercept(InterceptorManager.java:375)
dev_dataverse> at com.sun.ejb.containers.BaseContainer.__intercept(BaseContainer.java:4807)
dev_dataverse> at com.sun.ejb.containers.BaseContainer.intercept(BaseContainer.java:4795)
dev_dataverse> at com.sun.ejb.containers.EjbAsyncTask.call(EjbAsyncTask.java:101)
dev_dataverse> at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
dev_dataverse> at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
dev_dataverse> at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
dev_dataverse> at java.base/java.lang.Thread.run(Unknown Source)
dev_dataverse> |#]
dev_dataverse>
dev_dataverse> [#|2025-02-27T14:38:30.524+0000|WARNING|Payara 6.2024.6|org.eclipse.persistence.session./file:/opt/payara/deployments/dataverse/WEB-INF/classes/_VDCNet-ejbPU|_ThreadID=127;_ThreadName=http-thread-pool::http-listener-1(3);_TimeMillis=1740667110524;_LevelValue=900;|
dev_dataverse> java.lang.NullPointerException: Cannot invoke "org.eclipse.persistence.descriptors.DescriptorEvent.getDescriptor()" because "event" is null
dev_dataverse> at org.eclipse.persistence.internal.sessions.AbstractSession.executeDeferredEvents(AbstractSession.java:1479)
dev_dataverse> at org.eclipse.persistence.internal.sessions.UnitOfWorkImpl.internalExecuteQuery(UnitOfWorkImpl.java:3009)
dev_dataverse> at org.eclipse.persistence.internal.sessions.AbstractSession.executeQuery(AbstractSession.java:1841)
dev_dataverse> at org.eclipse.persistence.internal.sessions.AbstractSession.executeQuery(AbstractSession.java:1823)
dev_dataverse> at org.eclipse.persistence.internal.indirection.QueryBasedValueHolder.instantiate(QueryBasedValueHolder.java:136)
dev_dataverse> at org.eclipse.persistence.internal.indirection.QueryBasedValueHolder.instantiate(QueryBasedValueHolder.java:122)
dev_dataverse> at org.eclipse.persistence.internal.indirection.DatabaseValueHolder.getValue(DatabaseValueHolder.java:103)
dev_dataverse> at org.eclipse.persistence.internal.indirection.UnitOfWorkValueHolder.instantiateImpl(UnitOfWorkValueHolder.java:176)
dev_dataverse> at org.eclipse.persistence.internal.indirection.UnitOfWorkValueHolder.instantiate(UnitOfWorkValueHolder.java:244)
dev_dataverse> at org.eclipse.persistence.internal.indirection.DatabaseValueHolder.getValue(DatabaseValueHolder.java:103)
dev_dataverse> at org.eclipse.persistence.indirection.IndirectList.buildDelegate(IndirectList.java:275)
dev_dataverse> at org.eclipse.persistence.indirection.IndirectList.getDelegate(IndirectList.java:458)
dev_dataverse> at org.eclipse.persistence.indirection.IndirectList.isEmpty(IndirectList.java:542)
dev_dataverse> at edu.harvard.iq.dataverse.DatasetFieldType.isCompound(DatasetFieldType.java:444)
dev_dataverse> at edu.harvard.iq.dataverse.util.json.JsonPrinter.typeClassString(JsonPrinter.java:631)
dev_dataverse> at edu.harvard.iq.dataverse.util.json.JsonPrinter$DatasetFieldsToJson.startField(JsonPrinter.java:1134)
dev_dataverse> at edu.harvard.iq.dataverse.util.DatasetFieldWalker.walk(DatasetFieldWalker.java:81)
dev_dataverse> at edu.harvard.iq.dataverse.util.DatasetFieldWalker.walk(DatasetFieldWalker.java:102)
dev_dataverse> at edu.harvard.iq.dataverse.util.DatasetFieldWalker.walk(DatasetFieldWalker.java:63)
dev_dataverse> at edu.harvard.iq.dataverse.util.json.JsonPrinter.json(JsonPrinter.java:609)
dev_dataverse> at edu.harvard.iq.dataverse.util.json.JsonPrinter.jsonByBlocks(JsonPrinter.java:584)
dev_dataverse> at edu.harvard.iq.dataverse.util.json.JsonPrinter.jsonByBlocks(JsonPrinter.java:576)
dev_dataverse> at edu.harvard.iq.dataverse.util.json.JsonPrinter.json(JsonPrinter.java:491)
dev_dataverse> at edu.harvard.iq.dataverse.util.json.JsonPrinter.json(JsonPrinter.java:433)
dev_dataverse> at edu.harvard.iq.dataverse.api.Datasets.processDatasetUpdate(Datasets.java:1172)
dev_dataverse> at edu.harvard.iq.dataverse.api.Datasets.editVersionMetadata(Datasets.java:1058)
dev_dataverse> at edu.harvard.iq.dataverse.api.Datasets$Proxy$_$$_WeldSubclass.editVersionMetadata(Unknown Source)
dev_dataverse> at jdk.internal.reflect.GeneratedMethodAccessor471.invoke(Unknown Source)
dev_dataverse> at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
dev_dataverse> at java.base/java.lang.reflect.Method.invoke(Unknown Source)
dev_dataverse> at org.glassfish.jersey.server.model.internal.ResourceMethodInvocationHandlerFactory.lambda$static$0(ResourceMethodInvocationHandlerFactory.java:52)
dev_dataverse> at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher$1.run(AbstractJavaResourceMethodDispatcher.java:146)
dev_dataverse> at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.invoke(AbstractJavaResourceMethodDispatcher.java:189)
dev_dataverse> at org.glassfish.jersey.server.model.internal.JavaResourceMethodDispatcherProvider$ResponseOutInvoker.doDispatch(JavaResourceMethodDispatcherProvider.java:176)
dev_dataverse> at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.dispatch(AbstractJavaResourceMethodDispatcher.java:93)
dev_dataverse> at org.glassfish.jersey.server.model.ResourceMethodInvoker.invoke(ResourceMethodInvoker.java:478)
dev_dataverse> at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:400)
dev_dataverse> at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:81)
dev_dataverse> at org.glassfish.jersey.server.ServerRuntime$1.run(ServerRuntime.java:261)
dev_dataverse> at org.glassfish.jersey.internal.Errors$1.call(Errors.java:248)
dev_dataverse> at org.glassfish.jersey.internal.Errors$1.call(Errors.java:244)
dev_dataverse> at org.glassfish.jersey.internal.Errors.process(Errors.java:292)
dev_dataverse> at org.glassfish.jersey.internal.Errors.process(Errors.java:274)
dev_dataverse> at org.glassfish.jersey.internal.Errors.process(Errors.java:244)
dev_dataverse> at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:265)
dev_dataverse> at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:240)
dev_dataverse> at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:697)
dev_dataverse> at org.glassfish.jersey.servlet.WebComponent.serviceImpl(WebComponent.java:394)
dev_dataverse> at org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:346)
dev_dataverse> at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:357)
dev_dataverse> at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:311)
dev_dataverse> at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:205)
dev_dataverse> at org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1554)
dev_dataverse> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:331)
dev_dataverse> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:211)
dev_dataverse> at org.ocpsoft.rewrite.servlet.RewriteFilter.doFilter(RewriteFilter.java:226)
dev_dataverse> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:253)
dev_dataverse> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:211)
dev_dataverse> at edu.harvard.iq.dataverse.api.ApiBlockingFilter.doFilter(ApiBlockingFilter.java:170)
dev_dataverse> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:253)
dev_dataverse> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:211)
dev_dataverse> at edu.harvard.iq.dataverse.api.ApiRouter.doFilter(ApiRouter.java:31)
dev_dataverse> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:253)
dev_dataverse> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:211)
dev_dataverse> at org.apache.catalina.core.ApplicationDispatcher.doInvoke(ApplicationDispatcher.java:816)
dev_dataverse> at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:683)
dev_dataverse> at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:527)
dev_dataverse> at org.apache.catalina.core.ApplicationDispatcher.doDispatch(ApplicationDispatcher.java:497)
dev_dataverse> at org.apache.catalina.core.ApplicationDispatcher.dispatch(ApplicationDispatcher.java:379)
dev_dataverse> at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:329)
dev_dataverse> at edu.harvard.iq.dataverse.api.ApiRouter.doFilter(ApiRouter.java:35)
dev_dataverse> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:253)
dev_dataverse> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:211)
dev_dataverse> at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:257)
dev_dataverse> at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:166)
dev_dataverse> at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:757)
dev_dataverse> at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:577)
dev_dataverse> at com.sun.enterprise.web.WebPipeline.invoke(WebPipeline.java:99)
dev_dataverse> at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:158)
dev_dataverse> at org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:372)
dev_dataverse> at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:239)
dev_dataverse> at com.sun.enterprise.v3.services.impl.ContainerMapper$HttpHandlerCallable.call(ContainerMapper.java:520)
dev_dataverse> at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:217)
dev_dataverse> at org.glassfish.grizzly.http.server.HttpHandler.runService(HttpHandler.java:174)
dev_dataverse> at org.glassfish.grizzly.http.server.HttpHandler.doHandle(HttpHandler.java:153)
dev_dataverse> at org.glassfish.grizzly.http.server.HttpServerFilter.handleRead(HttpServerFilter.java:196)
dev_dataverse> at org.glassfish.grizzly.filterchain.ExecutorResolver$9.execute(ExecutorResolver.java:88)
dev_dataverse> at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:246)
dev_dataverse> at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:178)
dev_dataverse> at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:118)
dev_dataverse> at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:96)
dev_dataverse> at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:51)
dev_dataverse> at org.glassfish.grizzly.nio.transport.TCPNIOTransport.fireIOEvent(TCPNIOTransport.java:510)
dev_dataverse> at org.glassfish.grizzly.strategies.AbstractIOStrategy.fireIOEvent(AbstractIOStrategy.java:82)
dev_dataverse> at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.run0(WorkerThreadIOStrategy.java:83)
dev_dataverse> at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy$WorkerThreadRunnable.run(WorkerThreadIOStrategy.java:101)
dev_dataverse> at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:535)
dev_dataverse> at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.run(AbstractThreadPool.java:515)
dev_dataverse> at java.base/java.lang.Thread.run(Unknown Source)
dev_dataverse> |#]
dev_dataverse>
dev_dataverse> [#|2025-02-27T14:38:30.524+0000|WARNING|Payara 6.2024.6|org.eclipse.persistence.session./file:/opt/payara/deployments/dataverse/WEB-INF/classes/_VDCNet-ejbPU|_ThreadID=315;_ThreadName=__ejb-thread-pool15;_TimeMillis=1740667110524;_LevelValue=900;|
dev_dataverse> java.lang.NullPointerException: Cannot invoke "org.eclipse.persistence.descriptors.DescriptorEvent.getDescriptor()" because "event" is null
dev_dataverse> at org.eclipse.persistence.internal.sessions.AbstractSession.executeDeferredEvents(AbstractSession.java:1479)
dev_dataverse> at org.eclipse.persistence.internal.sessions.UnitOfWorkImpl.internalExecuteQuery(UnitOfWorkImpl.java:3009)
dev_dataverse> at org.eclipse.persistence.internal.sessions.AbstractSession.executeQuery(AbstractSession.java:1841)
dev_dataverse> at org.eclipse.persistence.internal.sessions.AbstractSession.executeQuery(AbstractSession.java:1823)
dev_dataverse> at org.eclipse.persistence.internal.indirection.NoIndirectionPolicy.valueFromQuery(NoIndirectionPolicy.java:352)
dev_dataverse> at org.eclipse.persistence.mappings.ForeignReferenceMapping.valueFromRowInternal(ForeignReferenceMapping.java:2343)
dev_dataverse> at org.eclipse.persistence.mappings.OneToOneMapping.valueFromRowInternal(OneToOneMapping.java:1874)
dev_dataverse> at org.eclipse.persistence.mappings.ForeignReferenceMapping.valueFromRow(ForeignReferenceMapping.java:2184)
dev_dataverse> at org.eclipse.persistence.mappings.ForeignReferenceMapping.buildCloneFromRow(ForeignReferenceMapping.java:341)
dev_dataverse> at org.eclipse.persistence.internal.descriptors.ObjectBuilder.buildAttributesIntoWorkingCopyClone(ObjectBuilder.java:2111)
dev_dataverse> at org.eclipse.persistence.internal.descriptors.ObjectBuilder.buildWorkingCopyCloneFromRow(ObjectBuilder.java:2364)
dev_dataverse> at org.eclipse.persistence.internal.descriptors.ObjectBuilder.buildObjectInUnitOfWork(ObjectBuilder.java:958)
dev_dataverse> at org.eclipse.persistence.internal.descriptors.ObjectBuilder.buildObjectInternal(ObjectBuilder.java:844)
dev_dataverse> at org.eclipse.persistence.internal.descriptors.ObjectBuilder.buildObject(ObjectBuilder.java:799)
dev_dataverse> at org.eclipse.persistence.internal.descriptors.ObjectBuilder.buildObject(ObjectBuilder.java:777)
dev_dataverse> at org.eclipse.persistence.queries.ObjectLevelReadQuery.buildObject(ObjectLevelReadQuery.java:863)
dev_dataverse> at org.eclipse.persistence.queries.ReadAllQuery.registerResultInUnitOfWork(ReadAllQuery.java:987)
dev_dataverse> at org.eclipse.persistence.queries.ReadAllQuery.executeObjectLevelReadQuery(ReadAllQuery.java:598)
dev_dataverse> at org.eclipse.persistence.queries.ObjectLevelReadQuery.executeDatabaseQuery(ObjectLevelReadQuery.java:1236)
dev_dataverse> at org.eclipse.persistence.queries.DatabaseQuery.execute(DatabaseQuery.java:913)
dev_dataverse> at org.eclipse.persistence.queries.ObjectLevelReadQuery.execute(ObjectLevelReadQuery.java:1195)
dev_dataverse> at org.eclipse.persistence.queries.ReadAllQuery.execute(ReadAllQuery.java:485)
dev_dataverse> at org.eclipse.persistence.queries.ObjectLevelReadQuery.executeInUnitOfWork(ObjectLevelReadQuery.java:1283)
dev_dataverse> at org.eclipse.persistence.internal.sessions.UnitOfWorkImpl.internalExecuteQuery(UnitOfWorkImpl.java:3008)
dev_dataverse> at org.eclipse.persistence.internal.sessions.AbstractSession.executeQuery(AbstractSession.java:1841)
dev_dataverse> at org.eclipse.persistence.internal.sessions.AbstractSession.executeQuery(AbstractSession.java:1823)
dev_dataverse> at org.eclipse.persistence.internal.indirection.QueryBasedValueHolder.instantiate(QueryBasedValueHolder.java:136)
dev_dataverse> at org.eclipse.persistence.internal.indirection.QueryBasedValueHolder.instantiate(QueryBasedValueHolder.java:122)
dev_dataverse> at org.eclipse.persistence.internal.indirection.DatabaseValueHolder.getValue(DatabaseValueHolder.java:103)
dev_dataverse> at org.eclipse.persistence.internal.indirection.UnitOfWorkValueHolder.instantiateImpl(UnitOfWorkValueHolder.java:176)
dev_dataverse> at org.eclipse.persistence.internal.indirection.UnitOfWorkValueHolder.instantiate(UnitOfWorkValueHolder.java:244)
dev_dataverse> at org.eclipse.persistence.internal.indirection.DatabaseValueHolder.getValue(DatabaseValueHolder.java:103)
dev_dataverse> at org.eclipse.persistence.indirection.IndirectList.buildDelegate(IndirectList.java:275)
dev_dataverse> at org.eclipse.persistence.indirection.IndirectList.getDelegate(IndirectList.java:458)
dev_dataverse> at org.eclipse.persistence.indirection.IndirectList$1.<init>(IndirectList.java:602)
dev_dataverse> at org.eclipse.persistence.indirection.IndirectList.listIterator(IndirectList.java:601)
dev_dataverse> at org.eclipse.persistence.indirection.IndirectList.iterator(IndirectList.java:560)
dev_dataverse> at edu.harvard.iq.dataverse.DatasetVersion.initDatasetFields(DatasetVersion.java:1626)
dev_dataverse> at edu.harvard.iq.dataverse.DatasetVersion.isValid(DatasetVersion.java:1759)
dev_dataverse> at edu.harvard.iq.dataverse.search.IndexServiceBean.toSolrDocs(IndexServiceBean.java:939)
dev_dataverse> at edu.harvard.iq.dataverse.search.IndexServiceBean.addOrUpdateDataset(IndexServiceBean.java:1748)
dev_dataverse> at edu.harvard.iq.dataverse.search.IndexServiceBean.addOrUpdateDataset(IndexServiceBean.java:920)
dev_dataverse> at edu.harvard.iq.dataverse.search.IndexServiceBean.doIndexDataset(IndexServiceBean.java:653)
dev_dataverse> at edu.harvard.iq.dataverse.search.IndexServiceBean.indexDataset(IndexServiceBean.java:474)
dev_dataverse> at edu.harvard.iq.dataverse.search.IndexServiceBean.doAsyncIndexDataset(IndexServiceBean.java:439)
dev_dataverse> at edu.harvard.iq.dataverse.search.IndexServiceBean.asyncIndexDataset(IndexServiceBean.java:423)
dev_dataverse> at jdk.internal.reflect.GeneratedMethodAccessor454.invoke(Unknown Source)
dev_dataverse> at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
dev_dataverse> at java.base/java.lang.reflect.Method.invoke(Unknown Source)
dev_dataverse> at org.glassfish.ejb.security.application.EJBSecurityManager.runMethod(EJBSecurityManager.java:588)
dev_dataverse> at org.glassfish.ejb.security.application.EJBSecurityManager.invoke(EJBSecurityManager.java:408)
dev_dataverse> at com.sun.ejb.containers.BaseContainer.invokeBeanMethod(BaseContainer.java:4835)
dev_dataverse> at com.sun.ejb.EjbInvocation.invokeBeanMethod(EjbInvocation.java:653)
dev_dataverse> at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:834)
dev_dataverse> at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:603)
dev_dataverse> at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.doCall(SystemInterceptorProxy.java:163)
dev_dataverse> at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.aroundInvoke(SystemInterceptorProxy.java:140)
dev_dataverse> at jdk.internal.reflect.GeneratedMethodAccessor191.invoke(Unknown Source)
dev_dataverse> at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
dev_dataverse> at java.base/java.lang.reflect.Method.invoke(Unknown Source)
dev_dataverse> at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:888)
dev_dataverse> at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:833)
dev_dataverse> at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:603)
dev_dataverse> at org.jboss.weld.module.ejb.AbstractEJBRequestScopeActivationInterceptor.aroundInvoke(AbstractEJBRequestScopeActivationInterceptor.java:81)
dev_dataverse> at org.jboss.weld.module.ejb.SessionBeanInterceptor.aroundInvoke(SessionBeanInterceptor.java:52)
dev_dataverse> at jdk.internal.reflect.GeneratedMethodAccessor171.invoke(Unknown Source)
dev_dataverse> at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
dev_dataverse> at java.base/java.lang.reflect.Method.invoke(Unknown Source)
dev_dataverse> at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:888)
dev_dataverse> at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:833)
dev_dataverse> at com.sun.ejb.containers.interceptors.InterceptorManager.intercept(InterceptorManager.java:375)
dev_dataverse> at com.sun.ejb.containers.BaseContainer.__intercept(BaseContainer.java:4807)
dev_dataverse> at com.sun.ejb.containers.BaseContainer.intercept(BaseContainer.java:4795)
dev_dataverse> at com.sun.ejb.containers.EjbAsyncTask.call(EjbAsyncTask.java:101)
dev_dataverse> at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
dev_dataverse> at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
dev_dataverse> at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
dev_dataverse> at java.base/java.lang.Thread.run(Unknown Source)
dev_dataverse> |#]
dev_dataverse>
dev_dataverse> [#|2025-02-27T14:38:30.525+0000|INFO|Payara 6.2024.6|edu.harvard.iq.dataverse.batch.util.LoggingUtil|_ThreadID=315;_ThreadName=__ejb-thread-pool15;_TimeMillis=1740667110525;_LevelValue=800;|
dev_dataverse> log directory: /opt/payara/appserver/glassfish/domains/domain1/logs/process-failures absent, trying to create|#]
dev_dataverse>
dev_dataverse> [#|2025-02-27T14:38:30.525+0000|INFO|Payara 6.2024.6|edu.harvard.iq.dataverse.batch.util.LoggingUtil|_ThreadID=315;_ThreadName=__ejb-thread-pool15;_TimeMillis=1740667110525;_LevelValue=800;|
dev_dataverse> log directory: /opt/payara/appserver/glassfish/domains/domain1/logs/process-failures created|#]
dev_dataverse>
dev_dataverse> [#|2025-02-27T14:38:30.534+0000|SEVERE|Payara 6.2024.6||_ThreadID=127;_ThreadName=http-thread-pool::http-listener-1(3);_TimeMillis=1740667110534;_LevelValue=1000;|
dev_dataverse> java.lang.NullPointerException: Cannot invoke "org.eclipse.persistence.descriptors.DescriptorEvent.getDescriptor()" because "event" is null
dev_dataverse> at org.eclipse.persistence.internal.sessions.AbstractSession.executeDeferredEvents(AbstractSession.java:1479)
dev_dataverse> at org.eclipse.persistence.internal.sessions.UnitOfWorkImpl.internalExecuteQuery(UnitOfWorkImpl.java:3009)
dev_dataverse> at org.eclipse.persistence.internal.sessions.AbstractSession.executeQuery(AbstractSession.java:1841)
dev_dataverse> at org.eclipse.persistence.internal.sessions.AbstractSession.executeQuery(AbstractSession.java:1823)
dev_dataverse> at org.eclipse.persistence.internal.indirection.QueryBasedValueHolder.instantiate(QueryBasedValueHolder.java:136)
dev_dataverse> at org.eclipse.persistence.internal.indirection.QueryBasedValueHolder.instantiate(QueryBasedValueHolder.java:122)
dev_dataverse> at org.eclipse.persistence.internal.indirection.DatabaseValueHolder.getValue(DatabaseValueHolder.java:103)
dev_dataverse> at org.eclipse.persistence.internal.indirection.UnitOfWorkValueHolder.instantiateImpl(UnitOfWorkValueHolder.java:176)
dev_dataverse> at org.eclipse.persistence.internal.indirection.UnitOfWorkValueHolder.instantiate(UnitOfWorkValueHolder.java:244)
dev_dataverse> at org.eclipse.persistence.internal.indirection.DatabaseValueHolder.getValue(DatabaseValueHolder.java:103)
dev_dataverse> at org.eclipse.persistence.indirection.IndirectList.buildDelegate(IndirectList.java:275)
dev_dataverse> at org.eclipse.persistence.indirection.IndirectList.getDelegate(IndirectList.java:458)
dev_dataverse> at org.eclipse.persistence.indirection.IndirectList.isEmpty(IndirectList.java:542)
dev_dataverse> at edu.harvard.iq.dataverse.DatasetFieldType.isCompound(DatasetFieldType.java:444)
dev_dataverse> at edu.harvard.iq.dataverse.util.json.JsonPrinter.typeClassString(JsonPrinter.java:631)
dev_dataverse> at edu.harvard.iq.dataverse.util.json.JsonPrinter$DatasetFieldsToJson.startField(JsonPrinter.java:1134)
dev_dataverse> at edu.harvard.iq.dataverse.util.DatasetFieldWalker.walk(DatasetFieldWalker.java:81)
dev_dataverse> at edu.harvard.iq.dataverse.util.DatasetFieldWalker.walk(DatasetFieldWalker.java:102)
dev_dataverse> at edu.harvard.iq.dataverse.util.DatasetFieldWalker.walk(DatasetFieldWalker.java:63)
dev_dataverse> at edu.harvard.iq.dataverse.util.json.JsonPrinter.json(JsonPrinter.java:609)
dev_dataverse> at edu.harvard.iq.dataverse.util.json.JsonPrinter.jsonByBlocks(JsonPrinter.java:584)
dev_dataverse> at edu.harvard.iq.dataverse.util.json.JsonPrinter.jsonByBlocks(JsonPrinter.java:576)
dev_dataverse> at edu.harvard.iq.dataverse.util.json.JsonPrinter.json(JsonPrinter.java:491)
dev_dataverse> at edu.harvard.iq.dataverse.util.json.JsonPrinter.json(JsonPrinter.java:433)
dev_dataverse> at edu.harvard.iq.dataverse.api.Datasets.processDatasetUpdate(Datasets.java:1172)
dev_dataverse> at edu.harvard.iq.dataverse.api.Datasets.editVersionMetadata(Datasets.java:1058)
dev_dataverse> at edu.harvard.iq.dataverse.api.Datasets$Proxy$_$$_WeldSubclass.editVersionMetadata(Unknown Source)
dev_dataverse> at jdk.internal.reflect.GeneratedMethodAccessor471.invoke(Unknown Source)
dev_dataverse> at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
dev_dataverse> at java.base/java.lang.reflect.Method.invoke(Unknown Source)
dev_dataverse> at org.glassfish.jersey.server.model.internal.ResourceMethodInvocationHandlerFactory.lambda$static$0(ResourceMethodInvocationHandlerFactory.java:52)
dev_dataverse> at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher$1.run(AbstractJavaResourceMethodDispatcher.java:146)
dev_dataverse> at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.invoke(AbstractJavaResourceMethodDispatcher.java:189)
dev_dataverse> at org.glassfish.jersey.server.model.internal.JavaResourceMethodDispatcherProvider$ResponseOutInvoker.doDispatch(JavaResourceMethodDispatcherProvider.java:176)
dev_dataverse> at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.dispatch(AbstractJavaResourceMethodDispatcher.java:93)
dev_dataverse> at org.glassfish.jersey.server.model.ResourceMethodInvoker.invoke(ResourceMethodInvoker.java:478)
dev_dataverse> at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:400)
dev_dataverse> at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:81)
dev_dataverse> at org.glassfish.jersey.server.ServerRuntime$1.run(ServerRuntime.java:261)
dev_dataverse> at org.glassfish.jersey.internal.Errors$1.call(Errors.java:248)
dev_dataverse> at org.glassfish.jersey.internal.Errors$1.call(Errors.java:244)
dev_dataverse> at org.glassfish.jersey.internal.Errors.process(Errors.java:292)
dev_dataverse> at org.glassfish.jersey.internal.Errors.process(Errors.java:274)
dev_dataverse> at org.glassfish.jersey.internal.Errors.process(Errors.java:244)
dev_dataverse> at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:265)
dev_dataverse> at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:240)
dev_dataverse> at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:697)
dev_dataverse> at org.glassfish.jersey.servlet.WebComponent.serviceImpl(WebComponent.java:394)
dev_dataverse> at org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:346)
dev_dataverse> at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:357)
dev_dataverse> at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:311)
dev_dataverse> at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:205)
dev_dataverse> at org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1554)
dev_dataverse> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:331)
dev_dataverse> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:211)
dev_dataverse> at org.ocpsoft.rewrite.servlet.RewriteFilter.doFilter(RewriteFilter.java:226)
dev_dataverse> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:253)
dev_dataverse> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:211)
dev_dataverse> at edu.harvard.iq.dataverse.api.ApiBlockingFilter.doFilter(ApiBlockingFilter.java:170)
dev_dataverse> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:253)
dev_dataverse> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:211)
dev_dataverse> at edu.harvard.iq.dataverse.api.ApiRouter.doFilter(ApiRouter.java:31)
dev_dataverse> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:253)
dev_dataverse> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:211)
dev_dataverse> at org.apache.catalina.core.ApplicationDispatcher.doInvoke(ApplicationDispatcher.java:816)
dev_dataverse> at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:683)
dev_dataverse> at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:527)
dev_dataverse> at org.apache.catalina.core.ApplicationDispatcher.doDispatch(ApplicationDispatcher.java:497)
dev_dataverse> at org.apache.catalina.core.ApplicationDispatcher.dispatch(ApplicationDispatcher.java:379)
dev_dataverse> at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:329)
dev_dataverse> at edu.harvard.iq.dataverse.api.ApiRouter.doFilter(ApiRouter.java:35)
dev_dataverse> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:253)
dev_dataverse> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:211)
dev_dataverse> at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:257)
dev_dataverse> at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:166)
dev_dataverse> at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:757)
dev_dataverse> at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:577)
dev_dataverse> at com.sun.enterprise.web.WebPipeline.invoke(WebPipeline.java:99)
dev_dataverse> at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:158)
dev_dataverse> at org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:372)
dev_dataverse> at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:239)
dev_dataverse> at com.sun.enterprise.v3.services.impl.ContainerMapper$HttpHandlerCallable.call(ContainerMapper.java:520)
dev_dataverse> at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:217)
dev_dataverse> at org.glassfish.grizzly.http.server.HttpHandler.runService(HttpHandler.java:174)
dev_dataverse> at org.glassfish.grizzly.http.server.HttpHandler.doHandle(HttpHandler.java:153)
dev_dataverse> at org.glassfish.grizzly.http.server.HttpServerFilter.handleRead(HttpServerFilter.java:196)
dev_dataverse> at org.glassfish.grizzly.filterchain.ExecutorResolver$9.execute(ExecutorResolver.java:88)
dev_dataverse> at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:246)
dev_dataverse> at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:178)
dev_dataverse> at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:118)
dev_dataverse> at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:96)
dev_dataverse> at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:51)
dev_dataverse> at org.glassfish.grizzly.nio.transport.TCPNIOTransport.fireIOEvent(TCPNIOTransport.java:510)
dev_dataverse> at org.glassfish.grizzly.strategies.AbstractIOStrategy.fireIOEvent(AbstractIOStrategy.java:82)
dev_dataverse> at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.run0(WorkerThreadIOStrategy.java:83)
dev_dataverse> at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy$WorkerThreadRunnable.run(WorkerThreadIOStrategy.java:101)
dev_dataverse> at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:535)
dev_dataverse> at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.run(AbstractThreadPool.java:515)
dev_dataverse> at java.base/java.lang.Thread.run(Unknown Source)
dev_dataverse> |#]
dev_dataverse>
dev_dataverse> [#|2025-02-27T14:38:30.534+0000|SEVERE|Payara 6.2024.6|edu.harvard.iq.dataverse.api.errorhandlers.ThrowableHandler|_ThreadID=127;_ThreadName=http-thread-pool::http-listener-1(3);_TimeMillis=1740667110534;_LevelValue=1000;|
dev_dataverse> _status="ERROR";_code=500;_message="Internal server error. More details available at the server logs.";_incidentId="8246160a-8486-46fc-8e93-c830b5a6e178";_interalError="NullPointerException";_requestUrl="http://localhost:8080/api/v1/datasets/:persistentId/editMetadata?persistentId=doi:10.5072/FK2/ZRZ4D5&replace=true";_requestMethod="PUT"||#]
dev_dataverse>
dev_dataverse> [#|2025-02-27T14:38:30.535+0000|SEVERE|Payara 6.2024.6|edu.harvard.iq.dataverse.api.errorhandlers.ThrowableHandler|_ThreadID=127;_ThreadName=http-thread-pool::http-listener-1(3);_TimeMillis=1740667110535;_LevelValue=1000;|
dev_dataverse> java.lang.NullPointerException: Cannot invoke "org.eclipse.persistence.descriptors.DescriptorEvent.getDescriptor()" because "event" is null
dev_dataverse> at org.eclipse.persistence.internal.sessions.AbstractSession.executeDeferredEvents(AbstractSession.java:1479)
dev_dataverse> at org.eclipse.persistence.internal.sessions.UnitOfWorkImpl.internalExecuteQuery(UnitOfWorkImpl.java:3009)
dev_dataverse> at org.eclipse.persistence.internal.sessions.AbstractSession.executeQuery(AbstractSession.java:1841)
dev_dataverse> at org.eclipse.persistence.internal.sessions.AbstractSession.executeQuery(AbstractSession.java:1823)
dev_dataverse> at org.eclipse.persistence.internal.indirection.QueryBasedValueHolder.instantiate(QueryBasedValueHolder.java:136)
dev_dataverse> at org.eclipse.persistence.internal.indirection.QueryBasedValueHolder.instantiate(QueryBasedValueHolder.java:122)
dev_dataverse> at org.eclipse.persistence.internal.indirection.DatabaseValueHolder.getValue(DatabaseValueHolder.java:103)
dev_dataverse> at org.eclipse.persistence.internal.indirection.UnitOfWorkValueHolder.instantiateImpl(UnitOfWorkValueHolder.java:176)
dev_dataverse> at org.eclipse.persistence.internal.indirection.UnitOfWorkValueHolder.instantiate(UnitOfWorkValueHolder.java:244)
dev_dataverse> at org.eclipse.persistence.internal.indirection.DatabaseValueHolder.getValue(DatabaseValueHolder.java:103)
dev_dataverse> at org.eclipse.persistence.indirection.IndirectList.buildDelegate(IndirectList.java:275)
dev_dataverse> at org.eclipse.persistence.indirection.IndirectList.getDelegate(IndirectList.java:458)
dev_dataverse> at org.eclipse.persistence.indirection.IndirectList.isEmpty(IndirectList.java:542)
dev_dataverse> at edu.harvard.iq.dataverse.DatasetFieldType.isCompound(DatasetFieldType.java:444)
dev_dataverse> at edu.harvard.iq.dataverse.util.json.JsonPrinter.typeClassString(JsonPrinter.java:631)
dev_dataverse> at edu.harvard.iq.dataverse.util.json.JsonPrinter$DatasetFieldsToJson.startField(JsonPrinter.java:1134)
dev_dataverse> at edu.harvard.iq.dataverse.util.DatasetFieldWalker.walk(DatasetFieldWalker.java:81)
dev_dataverse> at edu.harvard.iq.dataverse.util.DatasetFieldWalker.walk(DatasetFieldWalker.java:102)
dev_dataverse> at edu.harvard.iq.dataverse.util.DatasetFieldWalker.walk(DatasetFieldWalker.java:63)
dev_dataverse> at edu.harvard.iq.dataverse.util.json.JsonPrinter.json(JsonPrinter.java:609)
dev_dataverse> at edu.harvard.iq.dataverse.util.json.JsonPrinter.jsonByBlocks(JsonPrinter.java:584)
dev_dataverse> at edu.harvard.iq.dataverse.util.json.JsonPrinter.jsonByBlocks(JsonPrinter.java:576)
dev_dataverse> at edu.harvard.iq.dataverse.util.json.JsonPrinter.json(JsonPrinter.java:491)
dev_dataverse> at edu.harvard.iq.dataverse.util.json.JsonPrinter.json(JsonPrinter.java:433)
dev_dataverse> at edu.harvard.iq.dataverse.api.Datasets.processDatasetUpdate(Datasets.java:1172)
dev_dataverse> at edu.harvard.iq.dataverse.api.Datasets.editVersionMetadata(Datasets.java:1058)
dev_dataverse> at edu.harvard.iq.dataverse.api.Datasets$Proxy$_$$_WeldSubclass.editVersionMetadata(Unknown Source)
dev_dataverse> at jdk.internal.reflect.GeneratedMethodAccessor471.invoke(Unknown Source)
dev_dataverse> at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
dev_dataverse> at java.base/java.lang.reflect.Method.invoke(Unknown Source)
dev_dataverse> at org.glassfish.jersey.server.model.internal.ResourceMethodInvocationHandlerFactory.lambda$static$0(ResourceMethodInvocationHandlerFactory.java:52)
dev_dataverse> at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher$1.run(AbstractJavaResourceMethodDispatcher.java:146)
dev_dataverse> at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.invoke(AbstractJavaResourceMethodDispatcher.java:189)
dev_dataverse> at org.glassfish.jersey.server.model.internal.JavaResourceMethodDispatcherProvider$ResponseOutInvoker.doDispatch(JavaResourceMethodDispatcherProvider.java:176)
dev_dataverse> at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.dispatch(AbstractJavaResourceMethodDispatcher.java:93)
dev_dataverse> at org.glassfish.jersey.server.model.ResourceMethodInvoker.invoke(ResourceMethodInvoker.java:478)
dev_dataverse> at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:400)
dev_dataverse> at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:81)
dev_dataverse> at org.glassfish.jersey.server.ServerRuntime$1.run(ServerRuntime.java:261)
dev_dataverse> at org.glassfish.jersey.internal.Errors$1.call(Errors.java:248)
dev_dataverse> at org.glassfish.jersey.internal.Errors$1.call(Errors.java:244)
dev_dataverse> at org.glassfish.jersey.internal.Errors.process(Errors.java:292)
dev_dataverse> at org.glassfish.jersey.internal.Errors.process(Errors.java:274)
dev_dataverse> at org.glassfish.jersey.internal.Errors.process(Errors.java:244)
dev_dataverse> at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:265)
dev_dataverse> at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:240)
dev_dataverse> at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:697)
dev_dataverse> at org.glassfish.jersey.servlet.WebComponent.serviceImpl(WebComponent.java:394)
dev_dataverse> at org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:346)
dev_dataverse> at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:357)
dev_dataverse> at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:311)
dev_dataverse> at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:205)
dev_dataverse> at org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1554)
dev_dataverse> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:331)
dev_dataverse> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:211)
dev_dataverse> at org.ocpsoft.rewrite.servlet.RewriteFilter.doFilter(RewriteFilter.java:226)
dev_dataverse> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:253)
dev_dataverse> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:211)
dev_dataverse> at edu.harvard.iq.dataverse.api.ApiBlockingFilter.doFilter(ApiBlockingFilter.java:170)
dev_dataverse> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:253)
dev_dataverse> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:211)
dev_dataverse> at edu.harvard.iq.dataverse.api.ApiRouter.doFilter(ApiRouter.java:31)
dev_dataverse> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:253)
dev_dataverse> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:211)
dev_dataverse> at org.apache.catalina.core.ApplicationDispatcher.doInvoke(ApplicationDispatcher.java:816)
dev_dataverse> at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:683)
dev_dataverse> at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:527)
dev_dataverse> at org.apache.catalina.core.ApplicationDispatcher.doDispatch(ApplicationDispatcher.java:497)
dev_dataverse> at org.apache.catalina.core.ApplicationDispatcher.dispatch(ApplicationDispatcher.java:379)
dev_dataverse> at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:329)
dev_dataverse> at edu.harvard.iq.dataverse.api.ApiRouter.doFilter(ApiRouter.java:35)
dev_dataverse> at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:253)
dev_dataverse> at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:211)
dev_dataverse> at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:257)
dev_dataverse> at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:166)
dev_dataverse> at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:757)
dev_dataverse> at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:577)
dev_dataverse> at com.sun.enterprise.web.WebPipeline.invoke(WebPipeline.java:99)
dev_dataverse> at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:158)
dev_dataverse> at org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:372)
dev_dataverse> at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:239)
dev_dataverse> at com.sun.enterprise.v3.services.impl.ContainerMapper$HttpHandlerCallable.call(ContainerMapper.java:520)
dev_dataverse> at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:217)
dev_dataverse> at org.glassfish.grizzly.http.server.HttpHandler.runService(HttpHandler.java:174)
dev_dataverse> at org.glassfish.grizzly.http.server.HttpHandler.doHandle(HttpHandler.java:153)
dev_dataverse> at org.glassfish.grizzly.http.server.HttpServerFilter.handleRead(HttpServerFilter.java:196)
dev_dataverse> at org.glassfish.grizzly.filterchain.ExecutorResolver$9.execute(ExecutorResolver.java:88)
dev_dataverse> at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:246)
dev_dataverse> at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:178)
dev_dataverse> at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:118)
dev_dataverse> at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:96)
dev_dataverse> at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:51)
dev_dataverse> at org.glassfish.grizzly.nio.transport.TCPNIOTransport.fireIOEvent(TCPNIOTransport.java:510)
dev_dataverse> at org.glassfish.grizzly.strategies.AbstractIOStrategy.fireIOEvent(AbstractIOStrategy.java:82)
dev_dataverse> at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.run0(WorkerThreadIOStrategy.java:83)
dev_dataverse> at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy$WorkerThreadRunnable.run(WorkerThreadIOStrategy.java:101)
dev_dataverse> at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:535)
dev_dataverse> at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.run(AbstractThreadPool.java:515)
dev_dataverse> at java.base/java.lang.Thread.run(Unknown Source)
dev_dataverse> |#]
dev_dataverse>
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up โ it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Reproduce the 500 error with create-datasets-from-excel.py and follow the stack trace into DatasetVersion.initDatasetFields and isValid. Then inspect IndexServiceBean.toSolrDocs and the surrounding indexing flow to determine why the EclipseLink deferred event is null. Done means the dataset update no longer fails with this exception and the reported batch can complete.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- java
- Domain
- backend
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100