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Add classes for external sequencing data #308

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merged 3 commits into from
Feb 6, 2025

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@pkalita-lbl pkalita-lbl commented Feb 4, 2025

Fixes #258

Part of Milestone 6.7 (microbiomedata/issues#692)

The purpose of these changes is to add 4 new classes with corresponding SampleData slots. These classes are designed to presented in DataHarmonizer in the SubmissionPortal to capture information about externally-generated sequencing data. The 4 classes represent the cross product of analysis types (metagenomics and metatranscriptomics) and data formats (interleaved and non-interleaved).

For now we are only supporting data generated by Illumina models (among other restrictions). As far as the schema goes, this means a new enum (IlluminaInstrumentModelEnum) is being injected into the schema that represents only Illumina models. The new enum is built dynamically by a Python script (src/nmdc_submission_schema/scripts/instrument_enums.py) that looks at the InstrumentModelEnum from nmdc-schema and filters it down based on the presence of the string "Illumina" in an alias.

Aside from the new enum, the rest of the changes follow the standard process of defining elements unique to submission-schema in nmdc_submission_schema_base.yaml and then importing/modifying elements from nmdc-schema via sheets_and_friends.

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@pkalita-lbl pkalita-lbl marked this pull request as ready for review February 4, 2025 23:55
@pkalita-lbl pkalita-lbl requested review from aclum and turbomam February 4, 2025 23:56
@pkalita-lbl pkalita-lbl merged commit bc77d3e into main Feb 6, 2025
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@pkalita-lbl pkalita-lbl deleted the issue-258-add-external-sequencing-data-classes branch February 6, 2025 00:09
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Import DataGeneration and DataObject classes from nmdc-schema
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