Let the insdc_ingest_user submit data with missing required fields. #2281
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| @@ -513,7 +515,11 @@ def process_single( | |||
| ) | |||
| output_metadata[output_field] = processing_result.datum | |||
| # TODO(#2249): Do not throw an error if the submitter is insdc_ingest_user. | |||
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You could have also deleted the TODO. Seems to be done now ;)
| if ( | ||
| null_per_backend(processing_result.datum) | ||
| and spec.required | ||
| and unprocessed.inputMetadata["submitter"] != "insdc_ingest_user" |
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I was wondering whether it's actually a good idea to hardcode a username here? What if someone else installs an own Loculus instance with its own Keycloak, where that ingest user has a different name?
Wouldn't it be better to configure something like a "user that may submit broken data" list per config/Helm chart to the pipeline?
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resolves #2249
preview URL: https://insdc-ingest-user-allow-e.loculus.org/
Summary
Now that #2268 is merged we can add a check if the submitter is 'insdc_ingest_user' and not throw a required metadata field missing error if data from INSDC is missing required fields.
Screenshot and Tests
First test - check if the CCHF reference sequence is now in the database: NC_005301.3
Check that the number of sequences seen is comparable to the state of loculus prior to enforcement of field requirement, can be seen in the screenshot I took for this PR: fix(config): Add back required field to prepro #2243. We have 2 more sequences on CCHF and indeed there were 2 new releases on 2024-07-06. Also 18 new Mpox seqences from the 2024-07-09 and 1 new on the 2024-07-07. So the numbers match.