fixing a corrupted database

[Peter Kleiweg]

We are experiencing some issues that seem to be the result of data corruption.

What tools are available to check the integrety of the database, and fix any problems?

INCEpTION version 40.0

[Richard Eckart de Castilho]

Hello Peter,

> On 5. Oct 2026, at 16:22, Peter Kleiweg <peke...@gmail.com> wrote:
>
> We are experiencing some issues that seem to be the result of data corruption.

What kind of data corruption?

E.g. annotations are not stored in the database. They are stored in files.

> What tools are available to check the integrety of the database, and fix any problems?

There is the CAS Doctor in the project settings which analyzes the annotation data for
problems.

If you really have a problem with your database, then you might need to turn to whatever
tools your database system provides. What database are you using?

Best regards,

-- Richard

[Peter Kleiweg]

Op dinsdag 6 oktober 2026 om 07:55:44 UTC+2 schreef Richard Eckart de Castilho:

Hello Peter,

> On 5. Oct 2026, at 16:22, Peter Kleiweg <peke...@gmail.com> wrote:
>
> We are experiencing some issues that seem to be the result of data corruption.

What kind of data corruption?

E.g. annotations are not stored in the database. They are stored in files.

Database or stored files, I don't know which.

Problems we see:

- Annotators get error messages "Unable to render annotations."
- Users have state=FINISHED but annotatorState=IN_PROGRESS
- in the logs:
    -  Found curation CAS for document [...](...) but no annotation document
    - Due to mariadb SQL limitations, modifyDataType will lose primary key/autoincrement/not null/comment settings explicitly redefined in the change. Use <sql> or <modifySql> to re-specify all configuration if this is the case (after upgrading from 40.0 to 42.0)
    -  Unable to merge: The annotation already exists in the target document.

    - Unable to create span annotation: Curation is already finished. You can put it back into progress via the monitoring page.

    - Unable to render annotations for user

    - Unable to render: Type [webanno.custom.Dialogue] has no feature with name [Note]

 

> What tools are available to check the integrety of the database, and fix any problems?

There is the CAS Doctor in the project settings which analyzes the annotation data for
problems.

If you really have a problem with your database, then you might need to turn to whatever
tools your database system provides. What database are you using?

MariaDB. There is nothing wrong with the database itself, but it might contain incorrect data.

[Richard Eckart de Castilho]

Hello Peter,

the following message is a known issue although so far I am not aware that it
has caused any trouble.

> - Due to mariadb SQL limitations, modifyDataType will lose primary key/autoincrement/not null/comment settings explicitly redefined in the change. Use <sql> or <modifySql> to re-specify all configuration if this is the case (after upgrading from 40.0 to 42.0)

Regarding those messages:

> - Unable to merge: The annotation already exists in the target document.
> - Unable to create span annotation: Curation is already finished. You can put it back into progress via the monitoring page.

> - Found curation CAS for document [...](...) but no annotation document

... please make sure that the annotations your users want to work on
are not already in "curation in progress". Once a document is being
curated, users can no longer start working on them. You can take
a document out of being curated by right-clicking on the document
in the workload management in the curation column and selecting
reset. This will discard any potentially already made curations
though.

I assume you have already upgraded to 42.0. If that is the case,
errors like this

> - Annotators get error messages "Unable to render annotations."

> - Unable to render annotations for user

> - Unable to render: Type [webanno.custom.Dialogue] has no feature with name [Note]

... should no longer happen on read-only documents. Maybe those is a
older log lines?

Cheers,

-- Richard