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IHEC / ihec-ecosystems

This repo is for code and documentation associated with the ihec-ecosystems working group
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Sample attributes required? #72

Closed dzerbino closed 4 years ago

dzerbino commented 4 years ago

2 years ago we added this statement to the spec:

In order to pass IHEC metadata validation, all datasets submitted prior to 2018 must include all sample properties defined within each specific BIOMATERIAL_TYPE below.

This seems dubious. Should it not apply to submissions post 2018? Note that this change was not enforced in the JSON spec so this will catch people by surprise

sitag commented 4 years ago

@dzerbino

This seems dubious.

No. This is indeed true. If this is not being reflected in the json spec then that's up to @dbujold . I went back and filled everything for the March 2018 data freeze.

dzerbino commented 4 years ago

Hello @sitag ,

Thanks for all the background you sent me by email. To summarise:

In conclusion, if we don't want to trigger a massive resubmission of 2018 data we should remove this statement and mark as required each attribute which was present in the spec in 2018. This would be unambiguous and backwards compatible.

Do you agree?

dbujold commented 4 years ago

Yes, it makes sense to me, thanks.

martinhirst commented 4 years ago

I agree with @dzerbino.

I assume then the spec prior to 2018 is V1 and current is V1.1. This would make the distinction clear and the validation clean.

sitag commented 4 years ago

@dzerbino in 2018, i updated all our metadata to be v1.0 compliant for samples and experiments. i believe myrto was following up on other centres updating to v1.0; you may need to review myrto's notes on that.

dzerbino commented 4 years ago

Hello @sitag , IIRC, the plan is that Myrto did follow up on the centres to update to v1.0, but because the validator reports were not entirely clear, this has not been completed, effectively, this is what we are doing now.

sitag commented 4 years ago

@dzerbino i am certain that Myrto reached out to centres, but it's entirely possible that it was not finished. i believe @zxenia updated to validator were made a while back, so error messages should have been cleaned up since.