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 supported nested LinkML shapes into flat rows. See the support guide for depth limits and known mismatches.transforms.schema_diff— diffs two generated flat schemas so "what changed and why" is answerable.
Downstream ETL (the nmdc-lakehouse repo) is migrating to this package in PR #340. Until that change lands, its main branch still uses its local engine and saved schema.
Projection version 1.2.0 extracts TextValue raw strings into columns on the
containing record. Single values become strings and repeated values become
string arrays; TextValue-only child tables are removed.
Collection record types remain available for polymorphic dispatch. See the
TextValue projection contract for examples,
validation behavior, and migration from earlier artifacts.
Documentation Website
https://microbiomedata.github.io/nmdc-lakehouse-schema
Development and documentation
- Schema ownership, versions, Just syntax, and build/deploy workflow
- TextValue projection and migration
- Supported transformations, helper tables, and known data-loss boundaries
- Production TextValue and record-type audit
From an updated feature checkout:
just install
just generate-flat-schema
just check-flat-schema
just test
just test-dist
just gen-doc
uv run mkdocs build
A merge to main rebuilds and deploys documentation from the checked-in schema.
It does not regenerate that canonical artifact or publish a new Python package.
Run just --list to see available recipes and just --dry-run gen-doc to inspect
resolved documentation commands.
The source input is pinned to tagged nmdc-schema release 11.24.0. With
projection 1.2.0, the current target is 11.24.0+flat.1.2.0 and has 59 table
classes. See the upgrade guidance
for renamed fields, release verification, and production preflight requirements.
Repository structure
| Location | Purpose |
|---|---|
src/nmdc_lakehouse_schema/transforms/ |
Generator, runtime flattener, and schema-diff implementation. |
src/nmdc_lakehouse_schema/schema/nmdc_schema_flattened.yaml |
Canonical generated product; regenerate it instead of editing by hand. |
src/nmdc_lakehouse_schema/schema/nmdc_lakehouse_schema.yaml |
Remaining Person/PersonCollection template example; removal tracked in #16. |
src/nmdc_lakehouse_schema/datamodel/ |
Generated models for that template example, not the NMDC flat product. |
src/docs/ |
Authored documentation; edit these sources. |
docs/, site/ |
Ignored assembled Markdown and built HTML. |
tests/ |
Projection/artifact regression tests and remaining template fixtures. |
project/, examples/output/ |
Ignored output from template-generation/example recipes. |
Credits
This project uses the template linkml-project-copier.
1 maintainer
Metadata
1 maintainer
Release files for nmdc-lakehouse-schema 0.4.0
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