submission-schema

The NMDC submission schema.

Note that the while this repo is named submission-schema, the generated artifacts are named nmdc_submission_schema for disambiguation purposes when publishing to PyPI.

Website

• https://microbiomedata.github.io/submission-schema

Repository Structure

• examples/ - example data
• project/ - project files (do not edit these)
• src/ - source files (edit these)
  • nmdc_submission_schema
    • schema -- LinkML schema (edit this)
• datamodel -- Generated python datamodel
• tests - python tests

Developer Documentation

Updating the submission schema

The version of nmdc-schema used as a basis when building the submission schema is controlled by a dependency in the dev group, specified in pyproject.toml. You can update the version used by running:

uv add --group dev "nmdc-schema==X.Y.Z"  # replace X.Y.Z with the desired version

Note

It is important to use the == version constraint to ensure the exact version is installed.

Building the submission schema

Here's how you can generate the submission schema release artifacts:

Container-based process

Prerequisites

• Docker is installed on your computer
• You are in the root directory of the repository

Procedure

1. Build the container image you will later use to build the submission schema:

   docker build -t submission-schema-builder -f builder.Dockerfile .

2. If you haven't already done so (see the "Updating the submission schema" section above), use that container image to update the nmdc-schema dependency of the submission schema:

   docker run --rm -it -v ${PWD}:/submission-schema submission-schema-builder \
       uv add --group dev "nmdc-schema==X.Y.Z"  # replace X.Y.Z

   Then, rebuild the container image (so it has that new version of nmdc-schema installed):

   docker build -t submission-schema-builder -f builder.Dockerfile .

3. Use the container image to build the submission schema:

   docker run --rm -it -v ${PWD}:/submission-schema submission-schema-builder

4. Commit the changes, using the new nmdc-schema version number as the commit message; like this:

   git add .
   git commit -m "X.Y.Z"  # replace X.Y.Z with the nmdc-schema version

5. (Optional) Delete the container image:

   docker image rm submission-schema-builder

Direct process

Procedure

1. Install Python dependencies:

   uv sync

2. Generate the release artifacts:

   make clean all

3. Commit the changes, using the new nmdc-schema version number as the commit message; like this:

   git add .
   git commit -m "X.Y.Z"  # replace X.Y.Z with the nmdc-schema version

Credits

this project was made with linkml-project-cookiecutter