nmdc-lakehouse-schema
The NMDC flattened-schema product. It owns the definition of the flat, tabular shape the NMDC lakehouse writes to Parquet, independent of the data-generation, publication, and validation code that consumes it:
transforms.schema_generator— generates the flat LinkML target schema from a source schema (e.g.nmdc-schema).transforms.flatteners— the schema-driven flattener that turns nested LinkML records into flat rows, mirroring the generator's decision tree one-to-one.transforms.schema_diff— diffs two generated flat schemas so "what changed and why" is answerable.
Downstream ETL (the nmdc-lakehouse repo) depends on this package rather than defining the engine itself.
Documentation Website
https://microbiomedata.github.io/nmdc-lakehouse-schema
Repository Structure
- docs/ - mkdocs-managed documentation
- elements/ - generated schema documentation
- examples/ - Examples of using the schema
- project/ - project files (these files are auto-generated, do not edit)
- src/ - source files (edit these)
- nmdc_lakehouse_schema
- schema/ -- LinkML schema (edit this)
- datamodel/ -- generated Python datamodel
- nmdc_lakehouse_schema
- tests/ - Python tests
- data/ - Example data
Developer Tools
There are several pre-defined command-recipes available.
They are written for the command runner just.
To list all pre-defined commands, run just or just --list.
Credits
This project uses the template linkml-project-copier.
1 maintainer
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