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Berkeley schema ingest #1295
Berkeley schema ingest #1295
Commits on Aug 7, 2024
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Only pass necessary info to
upsert_doi
New slots were added to NMDC schema that breaks our current usage of the function.
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Update connection from sample to study
NMDC schema changed the slot that links a Biosample to a study. Previously the relationship was contained in the `part_of` slot on class `Biosample`. That slot has been renamed to `associated_studies`. Also, temporarily disable the backup link through omics_processing, as that relationship has changed in a more complex way.
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Don't use omics_processing during sample ingest
This isn't necessary since `associated_studies` is required and has cardinality of 1..*.
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Update ingest for data_generation objects
Formerly known as omics_procecssing records, there were some small schema tweaks that needed to be reflected in ingest. Note how the process of obtaining input biosamples is simpler since we now only need to query one collection of processes. This is a result of the change in database structure that puts related objects into the same collection.
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Note that this should be updated in the SQL schema to be optional/nullable.
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Extract instrument name from instrument collection
Note that in the future we might want to make instrument a fully fledged model in our database.
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