Publishing of Dataset does not work as expected (PID-Provider: Datacite) #11234
Labels
Type: Bug
a defect
Comments
|
Hmm - I think we just saw this (late last week) on a test machine when the DataCite provider is/was misconfigured. It looks like there’s a minor bug in the code when a DOI has not been created before publication. In short, an early step in publishing sets the datasetversion to 1.0 and a bug in the DOI creation code then has a bug when the version is not null that causes it to think a releaseDate exists when it doesn’t. I’ll submit a bug fix.
On the test machine we had, it appeared that fixing the DataCite provider fixed the issue, even for the existing stuck dataset, but that last part may have been miscommunication.
If your DataCite provider is working correctly now for new datasets (i.e. they get DOIs/don’t show the PID not registered warning/you can see the DOI in Fabrica), and the existing dataset still cannot be published, then I think a work-around would be to set the versionNumber to null in the draft version you are working with in the database and then make sure it is registered with DataCite before trying to publish again, e.g. using https://guides.dataverse.org/en/latest/api/native-api.html#reserve-a-pid.
Hope that helps,
…-- Jim
From: faborg ***@***.***>
Sent: Monday, February 10, 2025 5:47 AM
To: IQSS/dataverse ***@***.***>
Cc: Subscribed ***@***.***>
Subject: [IQSS/dataverse] Publishing of Dataset does not work as expected (PID-Provider: Datacite) (Issue #11234)
Hello,
We are currently experiencing an issue on Dataverse v6.4 where some datasets cannot be published. Our PID provider is DataCite.
I would greatly appreciate any support.
We are currently receiving the following log entries:
[2025-02-06T07:48:26.345+0100] [Payara 6.2024.6] [INFO] [] [edu.harvard.iq.dataverse.engine.command.impl.FinalizeDatasetPublicationCommand] [tid: _ThreadID=234 _ThreadName=__ejb-thread-pool1] [timeMillis: 1738824506345] [levelValue: 800] [[
Finalizing publication of the dataset doi:10.60776/U8CTRE]]
[2025-02-06T07:48:42.978+0100] [Payara 6.2024.6] [INFO] [] [edu.harvard.iq.dataverse.util.FileUtil] [tid: _ThreadID=234 _ThreadName=__ejb-thread-pool1] [timeMillis: 1738824522978] [levelValue: 800] [[
successfully validated DataFile 377; checksum fd76a5fa9a0ef4d9bd59d12ef67a5242]]
[2025-02-06T07:48:42.985+0100] [Payara 6.2024.6] [INFO] [] [edu.harvard.iq.dataverse.util.FileUtil] [tid: _ThreadID=234 _ThreadName=__ejb-thread-pool1] [timeMillis: 1738824522985] [levelValue: 800] [[
successfully validated DataFile 378; checksum c6330cb7465c9ac7b4fb924910f4a797]]
[2025-02-06T07:48:59.944+0100] [Payara 6.2024.6] [INFO] [] [edu.harvard.iq.dataverse.util.FileUtil] [tid: _ThreadID=234 _ThreadName=__ejb-thread-pool1] [timeMillis: 1738824539944] [levelValue: 800] [[
successfully validated DataFile 379; checksum cb005a5939961db2fd2eb6d2277ed1fc]]
[2025-02-06T07:49:00.762+0100] [Payara 6.2024.6] [WARNING] [] [edu.harvard.iq.dataverse.pidproviders.doi.datacite.DataCiteDOIProvider] [tid: _ThreadID=234 _ThreadName=__ejb-thread-pool1] [timeMillis: 1738824540762] [levelValue: 900] [[
Identifier not created: create failed
java.lang.NullPointerException: date must not be null
at java.base/java.util.Objects.requireNonNull(Objects.java:235)
at java.base/java.util.Calendar.setTime(Calendar.java:1792)
at java.base/java.text.SimpleDateFormat.format(SimpleDateFormat.java:978)
at java.base/java.text.SimpleDateFormat.format(SimpleDateFormat.java:971)
at java.base/java.text.DateFormat.format(DateFormat.java:378)
at edu.harvard.iq.dataverse.pidproviders.doi.XmlMetadataTemplate.writeDates(XmlMetadataTemplate.java:749)
at edu.harvard.iq.dataverse.pidproviders.doi.XmlMetadataTemplate.generateXML(XmlMetadataTemplate.java:128)
at edu.harvard.iq.dataverse.pidproviders.doi.XmlMetadataTemplate.generateXML(XmlMetadataTemplate.java:84)
at edu.harvard.iq.dataverse.pidproviders.doi.datacite.DOIDataCiteRegisterService.getMetadataFromDvObject(DOIDataCiteRegisterService.java:169)
at edu.harvard.iq.dataverse.pidproviders.doi.datacite.DOIDataCiteRegisterService.reserveIdentifier(DOIDataCiteRegisterService.java:62)
at edu.harvard.iq.dataverse.pidproviders.doi.datacite.DataCiteDOIProvider.createIdentifier(DataCiteDOIProvider.java:93)
at edu.harvard.iq.dataverse.engine.command.impl.AbstractDatasetCommand.registerExternalIdentifier(AbstractDatasetCommand.java:185)
at edu.harvard.iq.dataverse.engine.command.impl.FinalizeDatasetPublicationCommand.execute(FinalizeDatasetPublicationCommand.java:105)
at edu.harvard.iq.dataverse.engine.command.impl.FinalizeDatasetPublicationCommand.execute(FinalizeDatasetPublicationCommand.java:51)
at edu.harvard.iq.dataverse.EjbDataverseEngineInner.submit(EjbDataverseEngineInner.java:36)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:569)
at org.glassfish.ejb.security.application.EJBSecurityManager.runMethod(EJBSecurityManager.java:588)
at org.glassfish.ejb.security.application.EJBSecurityManager.invoke(EJBSecurityManager.java:408)
at com.sun.ejb.containers.BaseContainer.invokeBeanMethod(BaseContainer.java:4835)
at com.sun.ejb.EjbInvocation.invokeBeanMethod(EjbInvocation.java:653)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:834)
at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:603)
at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.doCall(SystemInterceptorProxy.java:163)
at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.aroundInvoke(SystemInterceptorProxy.java:140)
at jdk.internal.reflect.GeneratedMethodAccessor215.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:569)
at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:888)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:833)
at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:603)
at org.jboss.weld.module.ejb.AbstractEJBRequestScopeActivationInterceptor.aroundInvoke(AbstractEJBRequestScopeActivationInterceptor.java:72)
at org.jboss.weld.module.ejb.SessionBeanInterceptor.aroundInvoke(SessionBeanInterceptor.java:52)
at jdk.internal.reflect.GeneratedMethodAccessor204.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:569)
at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:888)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:833)
at com.sun.ejb.containers.interceptors.InterceptorManager.intercept(InterceptorManager.java:375)
at com.sun.ejb.containers.BaseContainer.__intercept(BaseContainer.java:4807)
at com.sun.ejb.containers.BaseContainer.intercept(BaseContainer.java:4795)
at com.sun.ejb.containers.EJBLocalObjectInvocationHandler.invoke(EJBLocalObjectInvocationHandler.java:212)
at com.sun.ejb.containers.EJBLocalObjectInvocationHandlerDelegate.invoke(EJBLocalObjectInvocationHandlerDelegate.java:90)
at jdk.proxy74/jdk.proxy74.$Proxy409.submit(Unknown Source)
at edu.harvard.iq.dataverse.__EJB31_Generated__EjbDataverseEngineInner__Intf____Bean__.submit(Unknown Source)
at edu.harvard.iq.dataverse.EjbDataverseEngine.submit(EjbDataverseEngine.java:283)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:569)
at org.glassfish.ejb.security.application.EJBSecurityManager.runMethod(EJBSecurityManager.java:588)
at org.glassfish.ejb.security.application.EJBSecurityManager.invoke(EJBSecurityManager.java:408)
at com.sun.ejb.containers.BaseContainer.invokeBeanMethod(BaseContainer.java:4835)
at com.sun.ejb.EjbInvocation.invokeBeanMethod(EjbInvocation.java:653)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:834)
at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:603)
at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.doCall(SystemInterceptorProxy.java:163)
at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.aroundInvoke(SystemInterceptorProxy.java:140)
at jdk.internal.reflect.GeneratedMethodAccessor215.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:569)
at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:888)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:833)
at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:603)
at org.jboss.weld.module.ejb.AbstractEJBRequestScopeActivationInterceptor.aroundInvoke(AbstractEJBRequestScopeActivationInterceptor.java:72)
at org.jboss.weld.module.ejb.SessionBeanInterceptor.aroundInvoke(SessionBeanInterceptor.java:52)
at jdk.internal.reflect.GeneratedMethodAccessor204.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:569)
at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:888)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:833)
at com.sun.ejb.containers.interceptors.InterceptorManager.intercept(InterceptorManager.java:375)
at com.sun.ejb.containers.BaseContainer.__intercept(BaseContainer.java:4807)
at com.sun.ejb.containers.BaseContainer.intercept(BaseContainer.java:4795)
at com.sun.ejb.containers.EJBLocalObjectInvocationHandler.invoke(EJBLocalObjectInvocationHandler.java:212)
at com.sun.ejb.containers.EJBLocalObjectInvocationHandlerDelegate.invoke(EJBLocalObjectInvocationHandlerDelegate.java:90)
at jdk.proxy74/jdk.proxy74.$Proxy365.submit(Unknown Source)
at edu.harvard.iq.dataverse.__EJB31_Generated__EjbDataverseEngine__Intf____Bean__.submit(Unknown Source)
at edu.harvard.iq.dataverse.DatasetServiceBean.callFinalizePublishCommandAsynchronously(DatasetServiceBean.java:964)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:569)
at org.glassfish.ejb.security.application.EJBSecurityManager.runMethod(EJBSecurityManager.java:588)
at org.glassfish.ejb.security.application.EJBSecurityManager.invoke(EJBSecurityManager.java:408)
at com.sun.ejb.containers.BaseContainer.invokeBeanMethod(BaseContainer.java:4835)
at com.sun.ejb.EjbInvocation.invokeBeanMethod(EjbInvocation.java:653)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:834)
at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:603)
at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.doCall(SystemInterceptorProxy.java:163)
at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.aroundInvoke(SystemInterceptorProxy.java:140)
at jdk.internal.reflect.GeneratedMethodAccessor215.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:569)
at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:888)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:833)
at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:603)
at org.jboss.weld.module.ejb.AbstractEJBRequestScopeActivationInterceptor.aroundInvoke(AbstractEJBRequestScopeActivationInterceptor.java:81)
at org.jboss.weld.module.ejb.SessionBeanInterceptor.aroundInvoke(SessionBeanInterceptor.java:52)
at jdk.internal.reflect.GeneratedMethodAccessor204.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:569)
at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:888)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:833)
at com.sun.ejb.containers.interceptors.InterceptorManager.intercept(InterceptorManager.java:375)
at com.sun.ejb.containers.BaseContainer.__intercept(BaseContainer.java:4807)
at com.sun.ejb.containers.BaseContainer.intercept(BaseContainer.java:4795)
at com.sun.ejb.containers.EjbAsyncTask.call(EjbAsyncTask.java:101)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:840)
]]
[2025-02-06T07:49:00.763+0100] [Payara 6.2024.6] [INFO] [] [edu.harvard.iq.dataverse.engine.command.impl.AbstractDatasetCommand] [tid: _ThreadID=234 _ThreadName=__ejb-thread-pool1] [timeMillis: 1738824540763] [levelValue: 800] [[
Call to globalIdServiceBean.createIdentifier failed: java.lang.NullPointerException: date must not be null]]
[2025-02-06T07:49:01.113+0100] [Payara 6.2024.6] [SEVERE] [] [edu.harvard.iq.dataverse.pidproviders.doi.datacite.DataCiteRESTfullClient] [tid: _ThreadID=234 _ThreadName=__ejb-thread-pool1] [timeMillis: 1738824541113] [levelValue: 1000] [[
Response from postMetadata: 422, DOI 10.60776/u8ctre: [facet 'enumeration'] The value 'Is Referenced By' is not an element of the set {'IsCitedBy', 'Cites', 'IsSupplementTo', 'IsSupplementedBy', 'IsContinuedBy', 'Continues', 'IsNewVersionOf', 'IsPreviousVersionOf', 'IsPartOf', 'HasPart', 'IsPublishedIn', 'IsReferencedBy', 'References', 'IsDocumentedBy', 'Documents', 'IsCompiledBy', 'Compiles', 'IsVariantFormOf', 'IsOriginalFormOf', 'IsIdenticalTo', 'HasMetadata', 'IsMetadataFor', 'Reviews', 'IsReviewedBy', 'IsDerivedFrom', 'IsSourceOf', 'Describes', 'IsDescribedBy', 'HasVersion', 'IsVersionOf', 'Requires', 'IsRequiredBy', 'Obsoletes', 'IsObsoletedBy', 'Collects', 'IsCollectedBy', 'HasTranslation', 'IsTranslationOf'}. at line 38, column 0]]
[2025-02-06T07:49:01.113+0100] [Payara 6.2024.6] [WARNING] [] [edu.harvard.iq.dataverse.pidproviders.doi.datacite.DataCiteDOIProvider] [tid: _ThreadID=234 _ThreadName=__ejb-thread-pool1] [timeMillis: 1738824541113] [levelValue: 900] [[
modifyMetadata failed: Response from postMetadata: 422, DOI 10.60776/u8ctre: [facet 'enumeration'] The value 'Is Referenced By' is not an element of the set {'IsCitedBy', 'Cites', 'IsSupplementTo', 'IsSupplementedBy', 'IsContinuedBy', 'Continues', 'IsNewVersionOf', 'IsPreviousVersionOf', 'IsPartOf', 'HasPart', 'IsPublishedIn', 'IsReferencedBy', 'References', 'IsDocumentedBy', 'Documents', 'IsCompiledBy', 'Compiles', 'IsVariantFormOf', 'IsOriginalFormOf', 'IsIdenticalTo', 'HasMetadata', 'IsMetadataFor', 'Reviews', 'IsReviewedBy', 'IsDerivedFrom', 'IsSourceOf', 'Describes', 'IsDescribedBy', 'HasVersion', 'IsVersionOf', 'Requires', 'IsRequiredBy', 'Obsoletes', 'IsObsoletedBy', 'Collects', 'IsCollectedBy', 'HasTranslation', 'IsTranslationOf'}. at line 38, column 0
java.io.IOException: Response from postMetadata: 422, DOI 10.60776/u8ctre: [facet 'enumeration'] The value 'Is Referenced By' is not an element of the set {'IsCitedBy', 'Cites', 'IsSupplementTo', 'IsSupplementedBy', 'IsContinuedBy', 'Continues', 'IsNewVersionOf', 'IsPreviousVersionOf', 'IsPartOf', 'HasPart', 'IsPublishedIn', 'IsReferencedBy', 'References', 'IsDocumentedBy', 'Documents', 'IsCompiledBy', 'Compiles', 'IsVariantFormOf', 'IsOriginalFormOf', 'IsIdenticalTo', 'HasMetadata', 'IsMetadataFor', 'Reviews', 'IsReviewedBy', 'IsDerivedFrom', 'IsSourceOf', 'Describes', 'IsDescribedBy', 'HasVersion', 'IsVersionOf', 'Requires', 'IsRequiredBy', 'Obsoletes', 'IsObsoletedBy', 'Collects', 'IsCollectedBy', 'HasTranslation', 'IsTranslationOf'}. at line 38, column 0
at edu.harvard.iq.dataverse.pidproviders.doi.datacite.DataCiteRESTfullClient.postMetadata(DataCiteRESTfullClient.java:174)
at edu.harvard.iq.dataverse.pidproviders.doi.datacite.DOIDataCiteRegisterService.registerIdentifier(DOIDataCiteRegisterService.java:74)
at edu.harvard.iq.dataverse.pidproviders.doi.datacite.DataCiteDOIProvider.publicizeIdentifier(DataCiteDOIProvider.java:209)
at edu.harvard.iq.dataverse.engine.command.impl.FinalizeDatasetPublicationCommand.publicizeExternalIdentifier(FinalizeDatasetPublicationCommand.java:416)
at edu.harvard.iq.dataverse.engine.command.impl.FinalizeDatasetPublicationCommand.execute(FinalizeDatasetPublicationCommand.java:216)
at edu.harvard.iq.dataverse.engine.command.impl.FinalizeDatasetPublicationCommand.execute(FinalizeDatasetPublicationCommand.java:51)
at edu.harvard.iq.dataverse.EjbDataverseEngineInner.submit(EjbDataverseEngineInner.java:36)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:569)
at org.glassfish.ejb.security.application.EJBSecurityManager.runMethod(EJBSecurityManager.java:588)
at org.glassfish.ejb.security.application.EJBSecurityManager.invoke(EJBSecurityManager.java:408)
at com.sun.ejb.containers.BaseContainer.invokeBeanMethod(BaseContainer.java:4835)
at com.sun.ejb.EjbInvocation.invokeBeanMethod(EjbInvocation.java:653)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:834)
at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:603)
at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.doCall(SystemInterceptorProxy.java:163)
at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.aroundInvoke(SystemInterceptorProxy.java:140)
at jdk.internal.reflect.GeneratedMethodAccessor215.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:569)
at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:888)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:833)
at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:603)
at org.jboss.weld.module.ejb.AbstractEJBRequestScopeActivationInterceptor.aroundInvoke(AbstractEJBRequestScopeActivationInterceptor.java:72)
at org.jboss.weld.module.ejb.SessionBeanInterceptor.aroundInvoke(SessionBeanInterceptor.java:52)
at jdk.internal.reflect.GeneratedMethodAccessor204.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:569)
at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:888)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:833)
at com.sun.ejb.containers.interceptors.InterceptorManager.intercept(InterceptorManager.java:375)
at com.sun.ejb.containers.BaseContainer.__intercept(BaseContainer.java:4807)
at com.sun.ejb.containers.BaseContainer.intercept(BaseContainer.java:4795)
at com.sun.ejb.containers.EJBLocalObjectInvocationHandler.invoke(EJBLocalObjectInvocationHandler.java:212)
at com.sun.ejb.containers.EJBLocalObjectInvocationHandlerDelegate.invoke(EJBLocalObjectInvocationHandlerDelegate.java:90)
at jdk.proxy74/jdk.proxy74.$Proxy409.submit(Unknown Source)
at edu.harvard.iq.dataverse.__EJB31_Generated__EjbDataverseEngineInner__Intf____Bean__.submit(Unknown Source)
at edu.harvard.iq.dataverse.EjbDataverseEngine.submit(EjbDataverseEngine.java:283)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:569)
at org.glassfish.ejb.security.application.EJBSecurityManager.runMethod(EJBSecurityManager.java:588)
at org.glassfish.ejb.security.application.EJBSecurityManager.invoke(EJBSecurityManager.java:408)
at com.sun.ejb.containers.BaseContainer.invokeBeanMethod(BaseContainer.java:4835)
at com.sun.ejb.EjbInvocation.invokeBeanMethod(EjbInvocation.java:653)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:834)
at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:603)
at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.doCall(SystemInterceptorProxy.java:163)
at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.aroundInvoke(SystemInterceptorProxy.java:140)
at jdk.internal.reflect.GeneratedMethodAccessor215.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:569)
at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:888)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:833)
at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:603)
at org.jboss.weld.module.ejb.AbstractEJBRequestScopeActivationInterceptor.aroundInvoke(AbstractEJBRequestScopeActivationInterceptor.java:72)
at org.jboss.weld.module.ejb.SessionBeanInterceptor.aroundInvoke(SessionBeanInterceptor.java:52)
at jdk.internal.reflect.GeneratedMethodAccessor204.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:569)
at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:888)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:833)
at com.sun.ejb.containers.interceptors.InterceptorManager.intercept(InterceptorManager.java:375)
at com.sun.ejb.containers.BaseContainer.__intercept(BaseContainer.java:4807)
at com.sun.ejb.containers.BaseContainer.intercept(BaseContainer.java:4795)
at com.sun.ejb.containers.EJBLocalObjectInvocationHandler.invoke(EJBLocalObjectInvocationHandler.java:212)
at com.sun.ejb.containers.EJBLocalObjectInvocationHandlerDelegate.invoke(EJBLocalObjectInvocationHandlerDelegate.java:90)
at jdk.proxy74/jdk.proxy74.$Proxy365.submit(Unknown Source)
at edu.harvard.iq.dataverse.__EJB31_Generated__EjbDataverseEngine__Intf____Bean__.submit(Unknown Source)
at edu.harvard.iq.dataverse.DatasetServiceBean.callFinalizePublishCommandAsynchronously(DatasetServiceBean.java:964)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:569)
at org.glassfish.ejb.security.application.EJBSecurityManager.runMethod(EJBSecurityManager.java:588)
at org.glassfish.ejb.security.application.EJBSecurityManager.invoke(EJBSecurityManager.java:408)
at com.sun.ejb.containers.BaseContainer.invokeBeanMethod(BaseContainer.java:4835)
at com.sun.ejb.EjbInvocation.invokeBeanMethod(EjbInvocation.java:653)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:834)
at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:603)
at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.doCall(SystemInterceptorProxy.java:163)
at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.aroundInvoke(SystemInterceptorProxy.java:140)
at jdk.internal.reflect.GeneratedMethodAccessor215.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:569)
at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:888)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:833)
at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:603)
at org.jboss.weld.module.ejb.AbstractEJBRequestScopeActivationInterceptor.aroundInvoke(AbstractEJBRequestScopeActivationInterceptor.java:81)
at org.jboss.weld.module.ejb.SessionBeanInterceptor.aroundInvoke(SessionBeanInterceptor.java:52)
at jdk.internal.reflect.GeneratedMethodAccessor204.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:569)
at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:888)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:833)
at com.sun.ejb.containers.interceptors.InterceptorManager.intercept(InterceptorManager.java:375)
at com.sun.ejb.containers.BaseContainer.__intercept(BaseContainer.java:4807)
at com.sun.ejb.containers.BaseContainer.intercept(BaseContainer.java:4795)
at com.sun.ejb.containers.EjbAsyncTask.call(EjbAsyncTask.java:101)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:840)
]]
[2025-02-06T07:49:01.114+0100] [Payara 6.2024.6] [WARNING] [] [edu.harvard.iq.dataverse.engine.command.impl.FinalizeDatasetPublicationCommand] [tid: _ThreadID=234 _ThreadName=__ejb-thread-pool1] [timeMillis: 1738824541114] [levelValue: 900] [[
Failed to publicize the identifier doi:10.60776/U8CTRE, or to publicize a file in the dataset; notifying the user(s), unlocking the dataset]]
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I was able to create a new Test-Dataset from scratch and publish it also. DOI registration also worked. The problem seems to be a value of the specific Dataset. What additional information can I provide to you to make the issue reproducible? Could the problem already be fixed in version 6.5 of Dataverse? We're running version 6.4 at the moment. Thanks for helping! |
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Per #11236, I think if you misconfigure DataCite, create a dataset so that it doesn't have a DOI, and then fix DataCite, you will still be unable to publish. The bug fix in the PR should handle the problem. The work-around would be as I suggested - delete the versionNumber from the db and make an API call to register the PID. Have you done that for the affected dataset? |
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Hello,
We are currently experiencing an issue on Dataverse v6.4 where some datasets cannot be published. Our PID provider is DataCite.
I would greatly appreciate any support.
We are currently receiving the following log entries:
The text was updated successfully, but these errors were encountered: