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Error When Accessing /api/admin/index/status Endpoint #11069

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ofahimIQSS opened this issue Dec 6, 2024 · 4 comments · Fixed by #11072
Closed

Error When Accessing /api/admin/index/status Endpoint #11069

ofahimIQSS opened this issue Dec 6, 2024 · 4 comments · Fixed by #11072
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@qqmyers
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Type: Bug a defect
Milestone
6.5

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@ofahimIQSS
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ofahimIQSS commented Dec 6, 2024 •
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Description
While testing in the internal environment, the following issue was encountered:

When running the command:

bash
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curl http://localhost:8080/api/admin/index/status
as documented in Solr Search Index Documentation, an error is logged in the server logs.

Steps to Reproduce

  1. Run the application on the internal environment.
  2. Execute the following command:
    curl http://localhost:8080/api/admin/index/status
  3. Observe the error in the server logs.

Expected Behavior
The endpoint should return the Solr indexing status without logging an error in the server logs.

Actual Behavior
An error is logged in the server.log. See the attached log excerpt for details.

Possible Cause
This may be a database-related issue. Further investigation is needed to confirm.

Environment
Commit: Using Develop branch [82dad99]
Environment: Internal
API Endpoint: /api/admin/index/status
Documentation: Solr Search Index Documentation
Observed Behavior: Error logged in server.log
Attachments
Error Log:
Issue server.log.txt
@ofahimIQSS ofahimIQSS added the Type: Bug a defect label Dec 6, 2024
@qqmyers qqmyers self-assigned this Dec 6, 2024
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qqmyers commented Dec 6, 2024

Looks like a bug - only in the status and orphan clearing though. Should have a fix soon. Introduced in #10710.

@qqmyers qqmyers mentioned this issue Dec 6, 2024
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@pdurbin pdurbin added this to the 6.5 milestone Dec 10, 2024
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pdurbin commented Dec 17, 2024

Observed Behavior: Error logged in server.log
Attachments
Error Log:
Issue server.log.txt

Here's part of the error:

jakarta.ejb.TransactionRolledbackLocalException: Exception thrown from bean: java.lang.IllegalArgumentException: An exception occurred while creating a query in EntityManager:
Exception Description: Syntax error parsing [SELECT fm.id FROM FileMetadata fm, DvObject dvo WHERE fm.datasetVersion.id=(SELECT dv.id FROM DatasetVersion dv WHERE dv.dataset.id=dvo.owner.id and dv.versionState=edu.harvard.iq.dataverse.DatasetVersion.VersionState.RELEASED ORDER BY dv.versionNumber DESC, dv.minorVersionNumber DESC LIMIT 1) AND dvo.id=fm.dataFile.id AND fm.dataFile.id=:fid].
[232, 232] The right parenthesis is missing from the sub-expression.
[291, 292] The ORDER BY clause has 'dv.minorVersionNumber DESC ' and 'LIMIT 1' that are not separated by a comma.
[292, 299] The order by item is not a valid expression.
[299, 350] The query contains a malformed ending.
at com.sun.ejb.containers.EJBContainerTransactionManager.checkExceptionClientTx(EJBContainerTransactionManager.java:615)
at com.sun.ejb.containers.EJBContainerTransactionManager.postInvokeTx(EJBContainerTransactionManager.java:485)
at com.sun.ejb.containers.BaseContainer.postInvokeTx(BaseContainer.java:4601)
at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:2134)
at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:2104)
at com.sun.ejb.containers.EJBLocalObjectInvocationHandler.invoke(EJBLocalObjectInvocationHandler.java:220)
at com.sun.ejb.containers.EJBLocalObjectInvocationHandlerDelegate.invoke(EJBLocalObjectInvocationHandlerDelegate.java:90)
at jdk.proxy156/jdk.proxy156.$Proxy1916.isInReleasedVersion(Unknown Source)
at edu.harvard.iq.dataverse.EJB31_Generated__DataFileServiceBean__Intf____Bean.isInReleasedVersion(Unknown Source)
at edu.harvard.iq.dataverse.search.IndexServiceBean.findPermissionsInSolrOnly(IndexServiceBean.java:2273)
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:568)
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.GeneratedMethodAccessor206.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
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:568)
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.proxy156/jdk.proxy156.$Proxy1921.findPermissionsInSolrOnly(Unknown Source)
at edu.harvard.iq.dataverse.search.EJB31_Generated__IndexServiceBean__Intf____Bean.findPermissionsInSolrOnly(Unknown Source)
at edu.harvard.iq.dataverse.search.IndexBatchServiceBean.getPermissionsInSolrButNotDatabase(IndexBatchServiceBean.java:340)
at edu.harvard.iq.dataverse.search.IndexBatchServiceBean.indexStatus(IndexBatchServiceBean.java:56)
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:568)
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.GeneratedMethodAccessor206.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
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:568)
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:833)
Caused by: java.lang.IllegalArgumentException: An exception occurred while creating a query in EntityManager:
Exception Description: Syntax error parsing [SELECT fm.id FROM FileMetadata fm, DvObject dvo WHERE fm.datasetVersion.id=(SELECT dv.id FROM DatasetVersion dv WHERE dv.dataset.id=dvo.owner.id and dv.versionState=edu.harvard.iq.dataverse.DatasetVersion.VersionState.RELEASED ORDER BY dv.versionNumber DESC, dv.minorVersionNumber DESC LIMIT 1) AND dvo.id=fm.dataFile.id AND fm.dataFile.id=:fid].
[232, 232] The right parenthesis is missing from the sub-expression.
[291, 292] The ORDER BY clause has 'dv.minorVersionNumber DESC ' and 'LIMIT 1' that are not separated by a comma.
[292, 299] The order by item is not a valid expression.
[299, 350] The query contains a malformed ending.
at org.eclipse.persistence.internal.jpa.EntityManagerImpl.createQuery(EntityManagerImpl.java:1728)
at com.sun.enterprise.container.common.impl.EntityManagerWrapper.createQuery(EntityManagerWrapper.java:458)
at edu.harvard.iq.dataverse.DataFileServiceBean.isInReleasedVersion(DataFileServiceBean.java:1410)
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:568)
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.GeneratedMethodAccessor206.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
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:568)
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)
... 71 more
Caused by: Exception [EclipseLink-0] (Eclipse Persistence Services - 4.0.1.payara-p2.v202310250827): org.eclipse.persistence.exceptions.JPQLException
Exception Description: Syntax error parsing [SELECT fm.id FROM FileMetadata fm, DvObject dvo WHERE fm.datasetVersion.id=(SELECT dv.id FROM DatasetVersion dv WHERE dv.dataset.id=dvo.owner.id and dv.versionState=edu.harvard.iq.dataverse.DatasetVersion.VersionState.RELEASED ORDER BY dv.versionNumber DESC, dv.minorVersionNumber DESC LIMIT 1) AND dvo.id=fm.dataFile.id AND fm.dataFile.id=:fid].
[232, 232] The right parenthesis is missing from the sub-expression.
[291, 292] The ORDER BY clause has 'dv.minorVersionNumber DESC ' and 'LIMIT 1' that are not separated by a comma.
[292, 299] The order by item is not a valid expression.
[299, 350] The query contains a malformed ending.
at org.eclipse.persistence.internal.jpa.jpql.HermesParser.buildException(HermesParser.java:159)
at org.eclipse.persistence.internal.jpa.jpql.HermesParser.validate(HermesParser.java:324)
at org.eclipse.persistence.internal.jpa.jpql.HermesParser.populateQueryImp(HermesParser.java:271)
at org.eclipse.persistence.internal.jpa.jpql.HermesParser.buildQuery(HermesParser.java:164)
at org.eclipse.persistence.internal.jpa.EJBQueryImpl.buildEJBQLDatabaseQuery(EJBQueryImpl.java:141)
at org.eclipse.persistence.internal.jpa.EJBQueryImpl.buildEJBQLDatabaseQuery(EJBQueryImpl.java:117)
at org.eclipse.persistence.internal.jpa.EJBQueryImpl.(EJBQueryImpl.java:104)
at org.eclipse.persistence.internal.jpa.EJBQueryImpl.(EJBQueryImpl.java:88)
at org.eclipse.persistence.internal.jpa.EntityManagerImpl.createQuery(EntityManagerImpl.java:1726)
... 102 more
]]

@pdurbin
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pdurbin commented Dec 17, 2024

As I mentioned in the Slack thread, this morning the same error...

Exception Description: Syntax error parsing [SELECT fm.id FROM FileMetadata fm, DvObject dvo WHERE fm.datasetVersion.id=(SELECT dv.id FROM DatasetVersion dv WHERE dv.dataset.id=dvo.owner.id and dv.versionState=edu.harvard.iq.dataverse.DatasetVersion.VersionState.RELEASED ORDER BY dv.versionNumber DESC, dv.minorVersionNumber DESC LIMIT 1) AND dvo.id=fm.dataFile.id AND fm.dataFile.id=:fid].
[232, 232] The right parenthesis is missing from the sub-expression.
[291, 292] The ORDER BY clause has 'dv.minorVersionNumber DESC ' and 'LIMIT 1' that are not separated by a comma.
[292, 299] The order by item is not a valid expression.
[299, 350] The query contains a malformed ending.

... was reported on Dataverse 6.4: https://dataverse.zulipchat.com/#narrow/channel/378866-troubleshooting/topic/Custom.20.E2.80.9CPerma.E2.80.9D.20PID.20Setup.20.26.20Indexing.20Problem/near/489483482

@pdurbin
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pdurbin commented Dec 17, 2024

reported on Dataverse 6.4

This makes sense because the fix at #11072 mentions that it's fixing code that was added in #10710 for 6.4.

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IQSS/11069 fix index status query QualitativeDataRepository/dataverse
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@pdurbin @qqmyers @ofahimIQSS