v6.0 upgrade: few datasets indexing failure - throws jakarta.persistence.NoResultException: getSingleResult()

[jeyala...@yahoo.com]

Hi!

   I was upgrading from v5.14 to v6.0 in our DEV env.

Following are versions we used:

Java 17

Payara : 6.2025.11 ( latest )

Solr: 9.10.0 ( latest )

During reindexing of Solr, it threw exception and stopped at one dataset (id: 4089250) indexing. 

We ran clear-orphans,  clear before starting indexing.

In the past (at v5.11.1), for the same dataset it threw exception, but progressed (see attached log).

While checking at DB, the dataset  (id: 4089250) was present in dvobject but not in dataset table. 

There are 3 such datasets all belonging to the same dataverse (id: 4089232).

We couldn't access the DEV website, throws internal server error. 

Please advise how to progress and complete the indexing.

How do we cleanup this one dataverse and its datasets at this state, without affecting any integrity.

Please find attached the logs of server.log. 

Thanks and regards,

Jeya

[Don Sizemore]

Hello,

The dataset table is a subclass of the dvobject table. May we see the output of SELECTs for those DB IDs from both tables?

Don

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[Jeyalakshmi Sambasivam]

Hi Don,

      Please see the selects for those IDs. 

Thanks and regards,

Jeya

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[Jeyalakshmi Sambasivam]

FYI, there was also "Internal Exception: org.postgresql.util.PSQLException: ERROR: estimateguestbookresponsetablesize() is not a procedure" exception is thrown (please see in attached Dev-indexing-exception-v6.0.txt file).

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[Jeyalakshmi Sambasivam]

Hi Don, 

          I am atttaching the specific logs of "Internal Exception: org.postgresql.util.PSQLException: ERROR: estimateguestbookresponsetablesize() is not a procedure" exception stack. These are thrown when we try to access the application website.

          Can please advise on possible causes of this?

Thanks and regards,

Jeya

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[James Myers]

The problem with the query is probably https://github.com/IQSS/dataverse/issues/11980 - Dataverse <6.9 isn’t compatible with Payara 6.2025.10+, https://github.com/IQSS/dataverse/pull/11827 contains the required fixes. The work-around would be to go back to an earlier version of Payara, e.g. 6.2025.9.

 

-- Jim

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[Jeyalakshmi Sambasivam]

Hi Jim,

      Thank you very much for your support always.

. In https://github.com/IQSS/dataverse/releases/v6.0 , upgrade to following are suggested:

  1.  Payara-6.2023.8

  2.  Solr, 9.3.0

We want to upgrade to higher versions of Payara and Solr that will be more secure and compatible with Dataverse 6.0.

In the latest Dataverse 6.8, following are used:

  1.  Payara 6.2025.3 (since Dataverse 6.7)

  2.  Solr 9.8.0 (since Dataverse 6.6)

Will the above versions be compatible with Dataverse 6.0?

Can you please advise on the highest possible Payara and Solr versions that we can upgrade to along with Dataverse 6.0?

Thanks and regards,

Jeya

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[jeyala...@yahoo.com]

Hello Jim,

       Thank you for your suggestion.

       According to your advice, we restored snapshot of v5.14 instance and upgraded our DEV env to v6.0 with again with:

        Payara-6.2025.9

        Solr-8.10.0

        Java 17
         
 Now the application  can come up. The Internal Exception: org.postgresql.util.PSQLException: ERROR: estimateguestbookresponsetablesize() is not a procedure" is gone.

 All dataverses were indexed.

 But the indexing stopped at the same problematic dataset 4089250 throwing attached exceptions.

The issue is : an entry is present in dvobject table for 4089250, but not in dataset table.

There are 3 such datasets: 4089250, 4089253 and 4089252

 Before upgrade, I tried to delete the owner dataverse of these entries, but we can't delete it as it says, the contents are not empty.

The contents are:

{"status":"OK","data":{"id":4089232,"alias":"testdaoist","name":"Test Daoist Dataverse","affiliation":"Nanyang Technological University","dataverseContacts":[{"displayOrder":0,"contactEmail":"shu...@ntu.edu.sg"}],"permissionRoot":true,"description":"This sub-dataverse is used to test the Daoist metadata block for customized metadata template.\n\nEdit 20220105","dataverseType":"RESEARCH_PROJECTS","ownerId":1,"creationDate":"2018-05-14T10:31:12Z"}}

Can please advise on cleaner way to get rid of this dataverse? Since dataverse is indexed and stopped at indexing 4089250 whether it is ok to clean up now? 

How do we proceed with our indexing passing these 3 entries indexing?

In v5.11.1 also, these issued dvobject entries were there, but the indexing progressed that time.

Thanks and regards,

Jeya

[James Myers]

Jeya,

 

Unfortunately, I don’t think we know – someone in the community might have tried upgrading those components and be able to give you some info, but there’s no comprehensive testing of forward compatibility with newer Payara, Solr, etc. that I know of.

 

One clue might be to look at the pull requests in which Dataverse updated the recommended Payara or Solr and see if there were code changes (beyond just updating the versions of those components.) If there were code changes in those PRs, earlier Dataverse releases are probably not compatible. For example, the issue Payara 6.2025.10 was their upgrade to a newer version of “EclipseLink” which had some backward incompatibilities and both the query that you saw fail and some mime-type related files had to be changed for Dataverse 6.9 which are in the #11827 PR I linked in the last email. However, no code changes in those PRs does not guarantee that earlier Dataverses are compatible.

 

FWIW: at QDR, we’ve been running ~v6.8 with Payara 6.2025.9 and Solr 9.9, but as QDR is a slight fork, I don’t know for sure that 6.8 or earlier Dataverses can run with those.

To view this discussion visit https://groups.google.com/d/msgid/dataverse-community/1572720745.4316.1765498821080%40mail.yahoo.com.

[James Myers]

 

 

From: 'jeyala...@yahoo.com' via Dataverse Users Community <dataverse...@googlegroups.com>
Sent: Friday, December 12, 2025 6:03 AM
To: Dataverse Users Community <dataverse...@googlegroups.com>
Subject: Re: [Dataverse-Users] v6.0 upgrade: few datasets indexing failure - throws jakarta.persistence.NoResultException: getSingleResult()

 

Jeya,

As Don said, datasets should have an entry in the dataset table and the dvobject table and, if they don’t, things will break. As far as I know, Dataverse should never get into this state, but a manual deletion of the dataset rows from the database would (I know QDR had some of these from early testing.). In any case, I think the only way to remove those datasets is to fully delete them in the database. Deleting the relevant rows from the dvobject table can be complex as there are foreign key relations to other tables, but it is possible to delete all the datasetversion, datasetfield and other entries tied to those datasets. Another approach might be to restore rows to the dataset table with those ids. If that was the only change, adding those rows could restore the datasets which you could then delete via the Dataverse UI if you don’t want them.

 

W.r.t. just being able to reindex – if you run reindexing with the /continue option, Dataverse will only index things that don’t have the lastindextime set. So – I think you might be able to just set the lastindex time on your failing datasets and use /continue to get past them.

 

And – the usual general caution – I don’t have full information and could be wrong, db editing is always risky, so definitely back-up before hand.

 

Hope that helps,

 

-- Jim

 

 

Hello Jim,

       Thank you for your suggestion.

       According to your advice, we restored snapshot of v5.14 instance and upgraded our DEV env to v6.0 with again with:

        Payara-6.2025.9

        Solr-8.10.0

        Java 17
         
 Now the application  can come up. The Internal Exception: org.postgresql.util.PSQLException: ERROR: estimateguestbookresponsetablesize() is not a procedure" is gone.

 

 All dataverses were indexed.

 But the indexing stopped at the same problematic dataset 4089250 throwing attached exceptions.

The issue is : an entry is present in dvobject table for 4089250, but not in dataset table.

There are 3 such datasets: 4089250, 4089253 and 4089252

 Before upgrade, I tried to delete the owner dataverse of these entries, but we can't delete it as it says, the contents are not empty.

 

To view this discussion visit https://groups.google.com/d/msgid/dataverse-community/151c8941-7e7e-4ce9-b1ef-e5c6acaff633n%40googlegroups.com.