feat(backend, ingest): Only return get-original-data when the aux-table is empty

[anna-parker]

resolves #

preview URL: https://check-aux-table.loculus.org/

Summary

As discussed in slack there is a period between when sequences are submitted and will be seen in get-original-data, in this period sequences are added to the aux tables. To prevent ingest errors we should not return original data while the backend is still processing sequences, e.g. there is data in the aux tables. When there is data in the aux tables get-original-data will respond with 423 LOCKED.

Also update ingest to wait 30seconds after a LOCKED response and then retry.
Also update ingest get-submitted to not add "" to dictionary when segment is missing and thus insdc_accession_segment does not exist.

Screenshot

Update I added a sequence to cchf that is why there is one sequence!

PR Checklist

• All necessary documentation has been adapted.
• The implemented feature is covered by an appropriate test.

[anna-parker]

I tried to add a test, e.g. but this fails as the auxtable is empty:

@Test
    fun `GIVEN still processing submitted data THEN return 503`() {
        convenienceClient.submitDefaultFiles(organism = organism)
        val response = submissionControllerClient.getOriginalMetadata()
        response.andExpect(status().isNotAvailable)
    }

[anna-parker]

CCHF ingest was stopped by this new 503 response:

14:46:45    ERROR call_loculus.py:get-submitted - Request failed:
URL: https://backend-check-aux-table.loculus.org/cchf/get-original-metadata
Method: GET
Status Code: 503
Response Content:

But sadly it doesn't seem like the ingest deployment is restarting

[theosanderson]

LGTM

(I can't see an easy way to add a test - if anyone does know how we can aim to do that)

[fengelniederhammer]

Testing it would have probably been possible by "manually" adding something to the aux tables. I.e. calling a function from the test that inserts a row to simulate being in the middle of an upload.

[corneliusroemer]

@fengelniederhammer makes sense. I'm just not familiar with the framework we're using here. Would be great if you could add such a test in a PR!