Pedigree info validation clean up #4636
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…idation-record-clean-up
jklugherz
reviewed
Feb 11, 2025
| request_json['vcfSamples'], search_dataset_type, | ||
| record_family_ids, affected_status_by_family, previous_loaded_individuals, sample_type, | ||
| ) | ||
| nonlocal loaded_individual_ids |
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I hadn't seen nonlocal before, I feel like personally it would be preferable to return these values from the nested function and do the updating of the loaded_sample_type and loaded_individual_ids via the returned values, but that's just style preference I guess and also I wouldn't request you change it here in this PR since you're just moving stuff around in here.
jklugherz
approved these changes
Feb 11, 2025
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The helper functions we use to validate pedigrees involve a lot of code duplication, in particular in the way that they look up potential existing individuals in the database. In order to implement #4580 we need better shared utilities for validating samples which was hard to do with the existing mess of validation. This cleans up the validation code and also abstracts out the logic used for validating the search sample subset into a single helper function.
This PR contains essentially no behavior changes- the only exception is that previously we did 2 steps to validate AnVIL loading requests and thats now done in one step, so certain requests now include more validation falures on the first pass instead of some failures and then more failures on the subsequent request after those are fixed