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Berkeley schema ingest #1295

Merged
merged 13 commits into from
Aug 7, 2024
Merged

Berkeley schema ingest #1295

merged 13 commits into from
Aug 7, 2024

Commits on Aug 7, 2024

  1. Only pass necessary info to upsert_doi 

    New slots were added to NMDC schema that breaks our current usage of the
function.
    @naglepuff
    naglepuff committed Aug 7, 2024
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  2. 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.
    @naglepuff
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  3. Don't use omics_processing during sample ingest 

    This isn't necessary since `associated_studies` is required and has
cardinality of 1..*.
    @naglepuff
    naglepuff committed Aug 7, 2024
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  4. 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.
    @naglepuff
    naglepuff committed Aug 7, 2024
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  5. Use subset of collection for pipeline ingest

    @naglepuff
    naglepuff committed Aug 7, 2024
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  6. Add default value for used 

    Note that this should be updated in the SQL schema to be
optional/nullable.
    @naglepuff
    naglepuff committed Aug 7, 2024
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  7. Extract instrument name from instrument collection 

    Note that in the future we might want to make instrument a fully
fledged model in our database.
    @naglepuff
    naglepuff committed Aug 7, 2024
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  8. Update nmdc workflow names enum

    @naglepuff
    naglepuff committed Aug 7, 2024
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  9. Update metatranscriptome workflow ingest

    @naglepuff
    naglepuff committed Aug 7, 2024
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  10. Remove unnecessary comment

    @naglepuff
    naglepuff committed Aug 7, 2024
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  11. Remove unused imports

    @naglepuff
    naglepuff committed Aug 7, 2024
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  12. Reduce use of raw string values during ingest

    @naglepuff
    naglepuff committed Aug 7, 2024
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  13. Rename variable for clarity

    @naglepuff
    naglepuff committed Aug 7, 2024
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