Add classes for external sequencing data #308
Merged
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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 theInstrumentModelEnum
fromnmdc-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
innmdc_submission_schema_base.yaml
and then importing/modifying elements fromnmdc-schema
viasheets_and_friends
.