Failure to submit due to duplicate and conflicting annotations

adina commented

2026-06-26 10:03:46 +00:00

Owner

[This is documenting notes from this hedgedoc in order to have them as proper issues. See also: #350 ]

Failure to submit due to duplicate and conflicting annotations

For some reason it can happen that the dumpthing auto-added record annotations start showing up twice (with identical tags, but different value) in a record. This then causes failure to resubmit such a record. The error message is a couple of pages long, and does not communicate to a non-expert that they must delete the annotations to not loose there work.

Musings

This is really painful, in particular because this is a self-made problem
I think dumpthings must stop doing anything to a record, if it cannot handle the consequences of this doing
Possibly this can all go away when a proper audit-trail feature is built. The submitter could then go into this trail, rather than into the DB record, where it causes these problems

Do I understand correctly that the error starts when dumpthings receives the record which now has "duplicate" annotation information? I.e. it is not that shacl-vue introduces the error? [name=jsheunis]

[This is documenting notes from this hedgedoc in order to have them as proper issues. See also: #350 ] ## Failure to submit due to duplicate and conflicting annotations For some reason it can happen that the dumpthing auto-added record annotations start showing up twice (with identical tags, but different value) in a record. This then causes failure to resubmit such a record. The error message is a couple of pages long, and does not communicate to a non-expert that they must delete the annotations to not loose there work. ### Musings - This is really painful, in particular because this is a self-made problem - I think dumpthings must stop doing anything to a record, if it cannot handle the consequences of this doing - Possibly this can all go away when a proper audit-trail feature is built. The submitter could then go into this trail, rather than into the DB record, where it causes these problems > Do I understand correctly that the error starts when dumpthings receives the record which now has "duplicate" annotation information? I.e. it is not that `shacl-vue` introduces the error? [name=jsheunis]

adina commented

2026-06-26 10:04:57 +00:00

Author

Owner

I believe this issue still persists, but I did not find a related issue here in the issue tracker. It would be good to have a description how the issue can be triggered and a copy of such an error.

jsheunis commented

2026-06-28 07:44:24 +00:00

Owner

Now that we have the audit backend in dumpthings, I believe the best course of action would be to remove the code in dumpthings that adds these annotations. Tagging @cmo.

I got an example error output (in shacl-vue browser console) from the chat:

status: 422, statusText: "", body: 'Conversion error: Conversion Format.ttl -> Format.json. Error: sio:SIO_001083: duplicate key, target class TRR379Person, ...

Previous comments from @mih on this:

However, the underlying issue does not appear to be caused by dumpthings (merely triggered). The underlying issue is that one record can be present in more than one place. shacl-vue "combines them and ends up creating annotation tags with duplicate keys where there must not be such

if there is a record in curated and one in incoming, they both have been submitted to dumpthings before. On that submission, dumpthings has added an annotation tag with the respective submission time. When the record is opened next, shacl-vue will get two different values for the same annotation tag. And it will represent that as two different statements (of course). And on resubmission, dumpthing (on behalf of linkml) rejects it, because there can only be one value per tag)

Now that we have the audit backend in dumpthings, I believe the best course of action would be to remove the code in dumpthings that adds these annotations. Tagging @cmo. I got an example error output (in shacl-vue browser console) from the chat: ``` status: 422, statusText: "", body: 'Conversion error: Conversion Format.ttl -> Format.json. Error: sio:SIO_001083: duplicate key, target class TRR379Person, ... ``` Previous comments from @mih on this: > However, the underlying issue does not appear to be caused by dumpthings (merely triggered). The underlying issue is that one record can be present in more than one place. shacl-vue "combines them and ends up creating annotation tags with duplicate keys where there must not be such > > if there is a record in curated and one in incoming, they both have been submitted to dumpthings before. On that submission, dumpthings has added an annotation tag with the respective submission time. When the record is opened next, shacl-vue will get two different values for the same annotation tag. And it will represent that as two different statements (of course). And on resubmission, dumpthing (on behalf of linkml) rejects it, because there can only be one value per tag)

mih commented

2026-06-28 10:18:32 +00:00

Owner

I agree and requested the same orinoco/dump-things-server#217

I agree and requested the same https://hub.psychoinformatics.de/orinoco/dump-things-server/issues/217

jsheunis commented

2026-06-28 19:21:13 +00:00

Owner

That feeling when you still agree with yourself from several months ago 😄

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Failure to submit due to duplicate and conflicting annotations #360

Failure to submit due to duplicate and conflicting annotations

Musings